GEO HTS Submission

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The steps are basically: (1) prepare the GEO HTS metadata spreadsheet, (2) upload files to GEO FTP, (3) submit the metadata file via the GEO web form, and (4) respond to any curator questions (esp. raw FASTQ).

1) Make a single dataset folder name for GEO (recommended)

GEO wants one folder per submission/dataset. Create one top-level folder name that will be uploaded as-is:

cd ~/Downloads
mv GEO_submissions GeoMx_DSP_M666_UKE_Hamburg

Inside it should remain:

dcc/
pkc/
annotation/
README.txt
counts_matrix.tsv

2) Prepare the GEO HTS metadata spreadsheet (REQUIRED)

On the GEO “Submit HTS” page:

Download the HTS metadata spreadsheet template.
Fill at least these tabs:

STUDY tab

Title, summary, overall design.
Add the “raw FASTQ missing” sentence if you still don’t have FASTQs:

Raw sequencing FASTQ files are currently not available to the authors; processed DCC outputs and PKC probe metadata are provided. FASTQs will be deposited to SRA and linked once obtained.

SAMPLES tab (most important)

One row per ROI/AOI (so ~45 rows for your DCCs).

Use Sample_ID (from your Sheet8/clean TSV) as the sample/library name.
For each row, set processed data file to the matching DCC filename (e.g., DSP-...-A02.dcc).
Include key sample characteristics (Group/Location/PCR/Case/etc.) from your annotation.

PROTOCOLS tab

Sample prep + GeoMx DSP workflow description.
Mention panels: Hs_R_NGS_WTA_v1.0, GeoMx_Hs_CTA_v1.0, GeoMx_COVID19_v1.0.
State: DCC exported from NanoString GeoMx NGS pipeline; PKC required to interpret RTS_IDs.

FILES / supplementary (if the template has it)

List:

all DCCs
all PKCs
the annotation file(s) (at least the clean TSV or the Excel)
README.txt
counts_matrix.tsv (optional, but you have it already)

Tip: In the metadata, reference counts_matrix.tsv as “gene-level raw counts matrix (targets x ROIs)” and keep DCCs as the authoritative per-ROI outputs.

3) FTP upload to GEO (data files only)

Connect to GEO’s FTP using the credentials/path GEO gives you (your personal upload directory).
In that upload directory, create a dataset folder, e.g.:
- GeoMx_DSP_M666_UKE_Hamburg/
Upload only the data files by FTP:
- the whole folder with subfolders: dcc/, pkc/, annotation/, plus README.txt, counts_matrix.tsv
Do NOT upload the metadata spreadsheet by FTP (GEO explicitly says upload metadata via the web form).

4) Submit the metadata spreadsheet on the GEO web page

After the FTP transfer finishes:

Go to Submit a new high-throughput sequencing submission
Upload the metadata spreadsheet file for this dataset
Submit → this places it in the GEO processing queue.

5) If GEO asks for raw FASTQs

This is the most common friction point for GeoMx when FASTQs aren’t available.

If they allow: they’ll accept processed now and ask you to link SRA later.
If they require: you’ll need to obtain FASTQs from the provider or email GEO and explain you only received DCC/PKC and are requesting FASTQs.

TODO: upload/paste the GEO HTS metadata spreadsheet template (blank) or a screenshot of the SAMPLES tab columns — to have a look which columns to fill with which fields from your annotation/M666_Sheet8_annotation_clean.tsv.

Comprehensive summary: GEO vs NCBI Submission Portal (SRA/BioProject/BioSample) for bulk RNA-seq + GeoMx DSP

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https://submit.ncbi.nlm.nih.gov/subs/

https://www.ncbi.nlm.nih.gov/geo/subs/

1) What each platform is best for

NCBI Submission Portal Used primarily to submit raw sequencing reads to the Sequence Read Archive (SRA) and to create/link the organizing records:
- BioProject (the overall study / project container)
- BioSample (the per-sample metadata records required for SRA)
NCBI GEO (Gene Expression Omnibus) Best for gene expression–style datasets and processed outputs, including:
- count matrices / processed tables
- sample/ROI metadata tables
- GeoMx DSP outputs (DCC/PKC)
- supplementary analysis outputs and documentation (README, workflow description) GEO is commonly used for “processed + metadata”, while raw FASTQs (if available) go to SRA.

2) Where to submit your two dataset types

Bulk RNA-seq (Illumina) with raw FASTQ files
- Submit to SRA via the NCBI Submission Portal.
- Ensure you have/define: BioProject + BioSamples, then upload FASTQs and metadata.
GeoMx DSP spatial transcriptomics with only DCC/PKC + annotation Excel (+ R workflow), no FASTQs
- Submit to GEO (not SRA), because DCC/PKC are processed outputs, not raw reads.
- In GEO, upload:
  - DCC files (processed counts + QC/metrics per ROI/AOI)
  - PKC files (panel/probe definitions)
  - annotation table (Excel is okay; CSV/TSV is even better for machine readability)
  - README describing file structure + column meanings + mapping between ROI IDs and metadata
  - analysis workflow (e.g., R scripts; optionally hosted on GitHub/Zenodo and linked)
If GeoMx FASTQs are obtained later
- Submit GeoMx FASTQs to SRA, and in the GEO record state: raw reads in SRA, processed data in GEO, cross-linking accessions.

3) What to choose in the NCBI “Start a new submission” list

For your use case:

Choose Sequence Read Archive (SRA) ✅ for FASTQ (raw reads).
You will also use/associate BioProject and BioSample (often created during the SRA workflow).
Do not use GenBank/TSA/Genome for these transcriptomics read submissions (those are for assembled sequences/genomes, not raw RNA-seq reads).
GEO is not started from that list; it has its own submission entry point.

4) Accounts / login clarification

Same login principle: In general, you use the same My NCBI account across NCBI services.
Why GEO can feel like “another account”:
- GEO requires a GEO Submitter Profile (contact identity/profile) attached to a My NCBI account.
- In many labs, a PI or colleague already has a GEO profile under their account—so the lab might say “GEO is on another account.”
Your options:
- Create/use your own My NCBI + GEO Submitter Profile and submit under your name.
- Or submit using the lab/PI account that already has the GEO profile (for consistent lab identity in GEO).

5) Practical “Data availability” logic for a manuscript

A journal-friendly setup is:

Raw sequencing reads (bulk RNA-seq FASTQs; later GeoMx FASTQs if available) → SRA accession(s)
Processed expression outputs and metadata (GeoMx DCC/PKC + annotation + processed tables) → GEO accession(s)
Workflow/code → GitHub + DOI archive (e.g., Zenodo), linked from GEO and/or the paper.

6) ENA note (from the email context)

If a manuscript currently lists an ENA project accession that can’t be found (e.g., looks like a placeholder), you either:
- confirm the correct existing ENA project accession, or
- create a new submission/accession (ENA or NCBI—both are widely accepted, but your processed GeoMx outputs still fit best in GEO).

7) Key takeaway (one-liner)

FASTQ = SRA (via NCBI Submission Portal + BioProject/BioSample)
GeoMx DCC/PKC + annotation + processed outputs = GEO
One My NCBI login, but GEO needs a GEO Submitter Profile and uses a separate submission entry point.

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德国《居留法》(AufenthG) §9 vs §18 中文译文与差异对比

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§ 9（定居许可 / Niederlassungserlaubnis）中文翻译

§9 定居许可（Niederlassungserlaubnis）

(1) 定居许可是一种无期限的居留许可。只有在本法明确允许的情形下，才可以附加附条件（附加条款）。§47不受影响。(sozialgesetzbuch-sgb.de)

(2) 向外国人应当签发定居许可，如果：(sozialgesetzbuch-sgb.de)

该外国人已持有居留许可（Aufenthaltserlaubnis）满五年；
其生活费用有保障；
已向法定养老保险缴纳至少 60 个月强制或自愿保险费，或能证明已为获得可比的养老待遇向保险/供养机构或保险公司支出；因育儿或居家护理造成的职业中断期应相应计入；
在综合考虑违反公共安全或秩序的严重程度/性质，或该外国人造成的危险，并考虑其既往居留时长以及其在德国境内的联系纽带后，不存在反对签发的公共安全或秩序方面的理由；
若其为雇员（受雇劳动者），其就业是被允许的；
其持有持续从事其职业活动所需的其他许可；
具备足够的德语能力；
具备对德国联邦境内的法律与社会制度及生活状况的基础知识；并且
对本人及与其共同生活的家庭成员拥有足够的居住空间。

（同一款后续规定）(sozialgesetzbuch-sgb.de)

第7、8项条件：如果成功完成融合课程（Integrationskurs），视为已证明。
若因身体、精神或心理疾病/残疾而无法满足第7、8项，可不再要求。
另外，为避免特殊困难（Härte），也可以不再要求第7、8项。
如果该外国人能够用德语以简单方式进行口头交流，并且其按照 §44 Abs.3 Nr.2没有参加融合课程的权利，或按照 §44a Abs.2 Nr.3不被强制参加融合课程，也可不再要求第7、8项。
此外，如果该外国人因前述“疾病/残疾”等原因也无法满足第2、3项，则也可不再要求第2、3项。

(3) 对处于婚姻共同生活的配偶：只要第(2)款第1句第3、5、6项由一方配偶满足即可。若该外国人正在接受可获得认可的学校/职业教育结业证书或大学学位的教育，则可不要求第(2)款第1句第3项（养老缴费/可比养老证明）。第1句在 §26 Abs.4的情形中同样适用。(sozialgesetzbuch-sgb.de)

(3a) 对于持有 §18c（专业人才定居许可）的外国人的配偶，应当签发定居许可，如果：(sozialgesetzbuch-sgb.de)

与该外国人处于婚姻共同生活；
已持有居留许可满三年；
每周工作不少于 20 小时；并且
满足第(2)款第1句第2项、第4至第9项条件。并且第(2)款第2至第6句相应适用；按第(3)款条件签发定居许可不受影响。

(4) 对签发定居许可所需的“持有居留许可”的期间，可计入：(sozialgesetzbuch-sgb.de)

曾经持有居留许可或定居许可的期间：如果该外国人在出境时持有定居许可，则可计入（但须扣除期间在德国境外、并导致定居许可失效的停留时间）；最多计入四年；
每次在德国境外停留且未导致居留许可失效的，可最多计入六个月；
以学习或职业教育为目的的合法居留时间，按一半计入。

§ 18（专业人才移民基本原则；一般规定）中文翻译

§18 专业人才移民基本原则；一般规定

(1) 接纳外国雇员，应以德国作为经济与科研所在地的需求为导向，并考虑劳动力市场状况。对外国专业人才和劳动力的特别机会，旨在保障专业/劳动力基础并加强社会保障体系。相关规定应以专业人才以及具有显著职业经验的劳动力在劳动力市场与社会中的可持续融入为目标，同时注意公共安全利益。(sozialgesetzbuch-sgb.de)

(2) 依据本节为从事就业活动签发居留许可的前提是：(sozialgesetzbuch-sgb.de)

存在明确的具体工作岗位/工作邀约；
联邦就业局（Bundesagentur für Arbeit）已按 §39同意；但若法律、国家间协议或《就业条例》（Beschäftigungsverordnung）规定可无需就业局同意即可就业，则不适用该同意要求；即便无需同意，如出现 §40 Abs.2 或 Abs.3中的某种情形，仍可拒绝签发居留许可；
如需要执业许可（Berufsausübungserlaubnis），则该许可已获签发或已获保证；
已确认资格等同性（Gleichwertigkeit），或存在被认可的外国高校学位、或与德国高校学位相当的外国高校学位——只要这属于签发居留许可的条件； 4a. 外国人与雇主共同声明该工作将被实际履行；并且
在首次签发 §18a 或 §18b 的情形中，如果外国人在满 45 岁之后申请，则工资至少达到法定养老保险年度缴费基数上限（Beitragsbemessungsgrenze）年值的 55%，除非能证明已有足够的养老保障。

同款后续：若存在对雇佣该外国人的公共利益（尤其地区性经济或劳动力市场政策利益），可在个案中对上述条件作例外处理，尤其是在工资门槛仅略低或年龄门槛仅略超时。内政部每年最晚于上一年 12 月 31 日在联邦公报公布当年的最低工资标准。(sozialgesetzbuch-sgb.de)

(3) 本法所称“专业人才（Fachkraft）”是指：(sozialgesetzbuch-sgb.de)

拥有德国境内的合格职业培训，或与之等同的外国职业资格（职业培训类专业人才）；或
拥有德国、被认可的外国，或与德国高校学位相当的外国高校学位（学术类专业人才）。

(4) 依据 §§18a、18b、18g、19c 签发的居留许可，期限为四年；如果劳动合同或就业局同意的期限更短，则按更短期限另加 3 个月，但总期限不得超过四年。(sozialgesetzbuch-sgb.de)

§9 和 §18 的核心区别（中文对比）

性质不同
- §9：定义并规定“定居许可/永居（无期限居留许可）”是什么，以及一般获得条件。(sozialgesetzbuch-sgb.de)
- §18：是“为了就业目的的居留许可体系”的总则/框架（专业人才移民原则、一般条件、专业人才定义、许可期限规则）。(sozialgesetzbuch-sgb.de)
期限不同
- §9：明确是“无期限居留许可”。(sozialgesetzbuch-sgb.de)
- §18：对应的多数就业类居留许可一般是有期限的（通常最长 4 年，或合同期+3个月但不超过4年）。(sozialgesetzbuch-sgb.de)
条件侧重点不同
- §9：强调“稳定融入与长期居留能力”的条件：5年居留、生活保障、60个月养老、语言、融入知识、住房、公共安全等。(sozialgesetzbuch-sgb.de)
- §18：强调“就业准入”的条件：具体工作邀约、就业局同意（或法定豁免）、必要执业许可、学历/资格认可、雇佣真实性声明，以及45岁后的工资/养老保障门槛等。(sozialgesetzbuch-sgb.de)
它们之间的关系
- 很多人的路径是：先在 §18 体系下拿到就业类居留许可（如 §18a/§18b/§18g 等），满足条件后再申请 §9（或某些人走 §18c 直接专业人才定居许可）。这一点从 §9(3a) 直接提到与 §18c 的关联也能看出来。(sozialgesetzbuch-sgb.de)

§18a 具备职业培训的专业人才（Fachkräfte mit Berufsausbildung）— 中文翻译

对“具备职业培训的专业人才”，应签发一项居留许可（Aufenthaltserlaubnis），用于从事任何合格的就业（qualifizierte Beschäftigung）。 (互联网法律)

§18b 具备高等教育背景的专业人才（Fachkräfte mit akademischer Ausbildung）— 中文翻译

对“具备高等教育背景的专业人才”，应签发一项居留许可（Aufenthaltserlaubnis），用于从事任何合格的就业（qualifizierte Beschäftigung）。 (sozialgesetzbuch-sgb.de)

§18c 专业人才的定居许可（Niederlassungserlaubnis für Fachkräfte）— 中文翻译

(1) 对专业人才，无需联邦就业局（BA）同意，应签发定居许可（Niederlassungserlaubnis），如果满足：

已持有 §18a / §18b / §18d 或 §18g 的居留身份满 3 年；
有一个工作岗位，且该岗位依 §18a/§18b/§18d/§18g 的条件允许由其担任；
已缴纳至少 36 个月法定养老保险强制或自愿缴费（或可比养老保障支出证明）；
具备足够的德语能力；
同时满足 §9 Abs.2 Satz1 Nr.2 以及 Nr.4–6、8、9 的条件（并适用 §9 的若干例外规则）。另外：若该专业人才在德国完成了职业培训或学业，上述第1项“3年”可缩短为 2年，第3项“36个月养老”可缩短为 24个月。 (sozialgesetzbuch-sgb.de)

(2) 作为蓝卡持有人（§18g），若已按 §18g 就业满 27个月并缴纳养老，且满足 §9 的相应条件，并具备“基础/简单德语”，则应签发定居许可；若德语达到“足够”，期限可缩短为 21个月。 (sozialgesetzbuch-sgb.de)

(3) 对“高度合格的、具备学术背景的专业人才”，在特殊情况下可（应当倾向于）在无需 BA 同意下签发定居许可：如果可以合理预期其能融入德国生活且无需国家救助即可维持生计，并满足 §9 Abs.2 Satz1 Nr.4（公共安全/秩序不构成反对理由）。各州还可规定此类签发需州最高主管机关（或其指定机构）同意。“高度合格”例示包括：具有特殊专业知识的科研人员；担任重要职务的教师/高级科研人员等。 (sozialgesetzbuch-sgb.de)

§18d 研究（Forschung）— 中文翻译

(1) 对外国人，无需 BA 同意，应依据欧盟指令 (EU) 2016/801 为“研究目的”签发居留许可，如果：

他： a) 与在德国境内为研究人员特殊准入程序而获得认可的研究机构，签署了有效的“接收协议”（Aufnahmevereinbarung）或相当合同，用于实施某项研究计划；或 b) 与从事研究的研究机构签署了有效接收协议或相当合同；并且
该研究机构书面承诺承担公共部门在接收协议结束后最长6个月内可能发生的费用，尤其包括： a) 该外国人在欧盟成员国非法停留期间的生活费用；以及 b) 对该外国人的遣返/驱逐费用。并且：在(1)第1项a)情形下，居留许可应在提出申请后 60天内签发。 (sozialgesetzbuch-sgb.de)

(2) 如果研究机构的活动主要由公共资金资助，则原则上应免除(1)第2项的费用承诺要求；若该研究项目具有特别公共利益，也可以免除。并规定相关承诺的适用条款。 (sozialgesetzbuch-sgb.de)

(3) 研究机构也可以向负责其认可的主管机构作出“通用承诺”，适用于与其签署接收协议并获得研究居留许可的所有外国人。 (sozialgesetzbuch-sgb.de)

(4) 该研究居留许可一般至少签发 1年；若参加带有流动措施的欧盟/多边项目，则至少 2年；若研究项目更短，则按项目期限签发，但在“至少2年”规则的情形下，期限仍至少 1年。 (sozialgesetzbuch-sgb.de)

(5) 依本条签发的居留许可，允许在接收协议所列研究机构开展研究，并允许从事教学活动；研究项目在居留期间变更，不当然导致该许可失效。 (sozialgesetzbuch-sgb.de)

(6) 对在欧盟某成员国已获国际保护的人，如其满足(1)条件且在该成员国获保护后已居留至少 2年，可签发研究目的居留许可；(5)相应适用。 (sozialgesetzbuch-sgb.de)

§18g 欧盟蓝卡（Blaue Karte EU）— 中文翻译

(1) 对具备学术背景的专业人才，无需 BA 同意，应为其签发欧盟蓝卡，用于从事与其资格相匹配的德国境内工作，前提是：其工资至少达到法定养老保险年度缴费基数上限的 50%，且不存在 §19f 规定的拒绝理由。但对以下两类人：

从事特定职业分类（ISCO-08若干组别所列职业）；或
在申请蓝卡前不超过 3年取得高校学位者；蓝卡改为需要 BA 同意签发，且工资门槛降低为年度缴费基数上限的 45.3%。并且：若申请人已持有 §18b 居留许可且蓝卡工作所需执业许可与 §18b 相同，则视为满足 §18 Abs.2 Nr.3；若其在 §18b 申请时已提交与蓝卡相同的学位，则视为满足 §18 Abs.2 Nr.4。另对等同高校学位、至少三年学制的高等教育项目毕业者，也可按相应规则适用。 (sozialgesetzbuch-sgb.de)

(2) 对不满足(1)的申请人，在某些职业组别（ISCO-08中的特定组别）下，可在需要 BA 同意的情况下签发蓝卡；并在一定条件下对学历要求作特殊处理（包括：工资至少45.3%；无§19f拒绝理由；并能证明近7年内获得的、至少3年的相关职业经验，且能力水平可与高校学位相当并对岗位必需）。 (sozialgesetzbuch-sgb.de)

(3) 签发蓝卡要求：具体工作邀约所约定的雇佣期限至少 6个月。 (sozialgesetzbuch-sgb.de)

(4) 蓝卡持有人更换雇主/岗位：一般不需要外国人局许可；但在就业的前 12个月，外国人局可将岗位变更暂停最多 30天并在此期间拒绝（若不再满足蓝卡签发条件）。 (sozialgesetzbuch-sgb.de)

(5) 在某些情况下，签发蓝卡可视为生活费已保障：如果外国人持有 §18a 或 §18b 的居留许可且不更换工作岗位。 (sozialgesetzbuch-sgb.de)

(6) 蓝卡延期的特殊工资门槛：若申请人在申请延期前不超过 3年取得学位，或自首次按较低门槛（(1)中45.3%那种情形）签发蓝卡以来未满 24个月，则延期时适用该较低门槛；其余仍适用一般延期规则。 (sozialgesetzbuch-sgb.de)

(7) 内政部每年在上一年 12月31日前于联邦公报公布下一年度(1)(2)所需的最低工资标准。 (sozialgesetzbuch-sgb.de)

五个条款的关键区别（中文对比）

§18a vs §18b（工作居留的入口）
- 都是“居留许可 Aufenthaltserlaubnis”用于合格就业；
- 差别主要在“你是职业培训型还是大学学历型专业人才”。 (互联网法律)
§18g（蓝卡）
- 仍是“居留许可”类型，但属于欧盟蓝卡路径；核心是学术背景 + 工资门槛（50% 或特定情形45.3%）以及对岗位变更的规则。 (sozialgesetzbuch-sgb.de)
§18d（研究）
- 也是“居留许可”，目的限定为研究；核心条件是接收协议/合同 + 研究机构费用承诺（以及相关豁免、期限规则）。 (sozialgesetzbuch-sgb.de)
§18c（定居/永居）
- 这是“定居许可 Niederlassungserlaubnis（无期限）”路径：一般要求你先持 §18a/18b/18d/18g 一段时间并满足养老、语言、§9相关条件；对蓝卡还有 27/21个月的加速路径。 (sozialgesetzbuch-sgb.de)

Protected: RND（Resistance–Nodulation–Division，耐药-结节-细胞分裂）外排泵确保鲍曼不动杆菌对人用靶向药物的固有耐受性

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FASTQ / raw sequencing datasets overview (T. and F.)

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1) Per-dataset sample inventory (compact lists)

1. `Data_Tam_RNAseq_2024_AUM_MHB_Urine_on_ATCC19606`

X101SC24105589-Z01-J001: AUM-1..3, MHB-1..3, Urine-1..3 (all PE)
X101SC25062155-Z01-J002: AUM-1..3, AUM-AZI-1..3, MH-1..3, MH-AZI-1..3, Urine-1..3, Urine-AZI-1..3 (all PE)

2. `Data_Tam_RNAseq_2025_LB-AB_IJ_W1_Y1_WT_vs_Mac-AB_IJ_W1_Y1_WT_on_ATCC19606`

LB: LB-AB-1..3, LB-IJ-(1,2,4), LB-W1-1..3, LB-WT19606-2..4, LB-Y1-2..4
Mac: Mac-AB-1..3, Mac-IJ-(1,2,4), Mac-W1-1..3, Mac-WT19606-2..4, Mac-Y1-2..4

3. `Data_Tam_RNAseq_2025_subMIC_exposure_on_ATCC19606`

Each with reps -1..-3 (all PE):

0_5ΔIJ-17, 0_5ΔIJ-24
preWT-17, preWT-24
preΔIJ-17, preΔIJ-24
WT0_5-17, WT0_5-24
WT-17, WT-24
ΔIJ-17, ΔIJ-24

4. `Data_Tam_DNAseq_2023_lab_strains`

A6WT – Acinetobacter baumannii ATCC19606
A10CraA – Acinetobacter baumannii ATCC19606
A12AYE – Acinetobacter baumannii AYE
A1917978 – Acinetobacter baumannii ATCC17978

5. `Data_Tam_DNAseq_2025_AYE-WT_Q_S_craA-Tig4_craA-1-Cm200_craA-2-Cm200`

AYE-Q, AYE-S, AYE-WTonTig4, AYE-craAonTig4, AYE-craA-1onCm200, AYE-craA-2onCm200, clinical (all PE)

6. `Data_Tam_DNAseq_2025_E.hormaechei-adeABadeIJ_adeIJK_CM1_CM2_on_ATCC19606`

adeABadeIJ, adeIJK, CM1, CM2, HF (all PE)

7. `Data_Tam_DNAseq_2025_ATCC19606-Y1Y2Y3Y4W1W2W3W4`

Illumina PE: △adeIJ, Tig1, Tig2, W, W2, W3, W4, Y, Y2, Y3, Y4
Nanopore (*_fastq_pass.tar):
- W1 (3 tar files), W2 (1), W3 (2), W4 (1)
- Y1 (3), Y2 (1), Y3 (1), Y4 (1)

8. `Data_Tam_DNAseq_2026_19606deltaIJfluE`

All PE; grouped by background:

19606△ABfluE: cef-1, cipro-2, dori-2, nitro-3, pip-1, polyB-3, tet-1
19606△IJfluE: cef-4, cipro-3, dori-1, nitro-3, pip-4, polyB-4
19606wtfluE: cef-1, cipro-2, dori-1, nitro-1, pip-4, polyB-4, tet-2

9. `Data_Tam_DNAseq_2026_Acinetobacter_harbinensis`

An6 (PE)

10. `Data_Tam_Metagenomics_2026`

A1, A1a, A2, B1, B2 (PE)

11. `Data_Foong_RNAseq_2021_ATCC19606_Cm` (mapping list provided)

Batch1: WT_1, WT_2B, C_1B, C_2, J_1, J_2
Batch2: Control, WT_1B, WT_2B, WT_3B, Cra_1, Cra_2, Cra_3, IJ_1B, IJ_2B, IJ_3
Batch3: adIJ_1, adIJ_2, crA2, crA_ab_1, crA_ab_2, crA_ab_3, adAB_1, adAB_2, adAB_ab1, adAB_ab2, adAB_ab3

12. `Data_Foong_DNAseq_2025_AYE_Dark_vs_Light`

Dark, Light (PE)

2) Dataset-level summary (quick lookup)

Dataset folder	Year	Data type	Platform / format	Run / project IDs present	Samples (n)	Files (n)	Sample groups / notes
`Data_Tam_RNAseq_2024_AUM_MHB_Urine_on_ATCC19606/`	2024	RNA-seq	Illumina PE (`_1.fq.gz`, `_2.fq.gz`)	`X101SC24105589-Z01-J001`, `X101SC25062155-Z01-J002`	27	54	J001: AUM/MHB/Urine (each 1–3). J002: AUM, AUM-AZI, MH, MH-AZI, Urine, Urine-AZI (each 1–3).
`Data_Tam_RNAseq_2025_LB-AB_IJ_W1_Y1_WT_vs_Mac-AB_IJ_W1_Y1_WT_on_ATCC19606/`	2025	RNA-seq	Illumina PE	`X101SC25015922-Z02-J002`	30	60	LB vs Mac sets; conditions AB, IJ, W1, Y1, WT19606 with listed replicates (mostly 1–3 or 2–4; IJ uses 1,2,4).
`Data_Tam_RNAseq_2025_subMIC_exposure_on_ATCC19606/`	2025	RNA-seq	Illumina PE	`X101SC25062155-Z01-J001`	36	72	12 condition blocks × 3 reps: `preWT`, `preΔIJ`, `WT`, `ΔIJ`, `WT0_5`, `0_5ΔIJ` at timepoints `17` and `24`.
`Data_Tam_DNAseq_2025_ATCC19606-Y1Y2Y3Y4W1W2W3W4/`	2025	DNA-seq	Illumina PE + Nanopore (`*_fastq_pass.tar`)	Illumina: `X101SC24065637-Z01-J001/J002`; Nanopore: `X101SC25080408-Z01-J001`	11 (Illumina) + 13 tar archives	22 + 13	Illumina: `△adeIJ`, `Tig1`, `Tig2`, `W`, `W2–W4`, `Y`, `Y2–Y4`. Nanopore: W1(3), W2(1), W3(2), W4(1), Y1(3), Y2(1), Y3(1), Y4(1) tar files.
`Data_Tam_DNAseq_2025_AYE-WT_Q_S_craA-Tig4_craA-1-Cm200_craA-2-Cm200/`	2025	DNA-seq	Illumina PE	`X101SC25015922-Z01-J001`	7	14	AYE variants: `AYE-Q`, `AYE-S`, `AYE-WTonTig4`, `AYE-craAonTig4`, `AYE-craA-1onCm200`, `AYE-craA-2onCm200`, plus `clinical`.
`Data_Tam_DNAseq_2025_E.hormaechei-adeABadeIJ_adeIJK_CM1_CM2`	2025	DNA-seq	Illumina PE	`X101SC24115801-Z01-J001`	5	10	`adeABadeIJ`, `adeIJK`, `CM1`, `CM2`, `HF`.
`Data_Tam_DNAseq_2026_19606deltaIJfluE/`	2026	DNA-seq	Illumina PE	`X101SC25116512-Z01-J003`	20	40	Three backgrounds: `19606△ABfluE` (7), `19606△IJfluE` (6), `19606wtfluE*` (7) across drug tags (cef/cipro/dori/nitro/pip/polyB/tet) with replicate suffixes.
`Data_Tam_DNAseq_2026_Acinetobacter_harbinensis/`	2026	DNA-seq	Illumina PE	`X101SC25116512-Z01-J002`	1	2	`An6` (paired-end).
`Data_Tam_Metagenomics_2026/`	2026	Metagenomics	Illumina PE	`X101SC25123808-Z01-J001`	5	10	`A1`, `A1a`, `A2`, `B1`, `B2`.
`Data_Foong_RNAseq_2021_ATCC19606_Cm/`	2021	RNA-seq	Illumina PE (symlink/mapping list shown)	(paths point to `raw_data_batch1/2/3`)	27	54	Batch1: WT/craA/adeIJ (each 2 reps). Batch2: Control + WT.abx + craA.abx + adeIJ.abx (various reps). Batch3: adeIJ, craA, craA.abx, adeAB, adeAB.abx (various reps).
`Data_Foong_DNAseq_2025_AYE_Dark_vs_Light/`	2025	DNA-seq	Illumina PE	`X101SC25116512-Z01-J001`	2	4	`Dark`, `Light`.

3) Complete list


Data_Tam_RNAseq_2024_AUM_MHB_Urine_on_ATCC19606/

    ./X101SC24105589-Z01-J001/01.RawData/AUM-1/AUM-1_1.fq.gz
    ./X101SC24105589-Z01-J001/01.RawData/AUM-1/AUM-1_2.fq.gz
    ./X101SC24105589-Z01-J001/01.RawData/AUM-2/AUM-2_1.fq.gz
    ./X101SC24105589-Z01-J001/01.RawData/AUM-2/AUM-2_2.fq.gz
    ./X101SC24105589-Z01-J001/01.RawData/AUM-3/AUM-3_1.fq.gz
    ./X101SC24105589-Z01-J001/01.RawData/AUM-3/AUM-3_2.fq.gz
    ./X101SC24105589-Z01-J001/01.RawData/MHB-1/MHB-1_1.fq.gz
    ./X101SC24105589-Z01-J001/01.RawData/MHB-1/MHB-1_2.fq.gz
    ./X101SC24105589-Z01-J001/01.RawData/MHB-2/MHB-2_1.fq.gz
    ./X101SC24105589-Z01-J001/01.RawData/MHB-2/MHB-2_2.fq.gz
    ./X101SC24105589-Z01-J001/01.RawData/MHB-3/MHB-3_1.fq.gz
    ./X101SC24105589-Z01-J001/01.RawData/MHB-3/MHB-3_2.fq.gz
    ./X101SC24105589-Z01-J001/01.RawData/Urine-1/Urine-1_1.fq.gz
    ./X101SC24105589-Z01-J001/01.RawData/Urine-1/Urine-1_2.fq.gz
    ./X101SC24105589-Z01-J001/01.RawData/Urine-2/Urine-2_1.fq.gz
    ./X101SC24105589-Z01-J001/01.RawData/Urine-2/Urine-2_2.fq.gz
    ./X101SC24105589-Z01-J001/01.RawData/Urine-3/Urine-3_1.fq.gz
    ./X101SC24105589-Z01-J001/01.RawData/Urine-3/Urine-3_2.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/AUM-1/AUM-1_1.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/AUM-1/AUM-1_2.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/AUM-2/AUM-2_1.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/AUM-2/AUM-2_2.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/AUM-3/AUM-3_1.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/AUM-3/AUM-3_2.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/AUM-AZI-1/AUM-AZI-1_1.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/AUM-AZI-1/AUM-AZI-1_2.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/AUM-AZI-2/AUM-AZI-2_1.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/AUM-AZI-2/AUM-AZI-2_2.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/AUM-AZI-3/AUM-AZI-3_1.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/AUM-AZI-3/AUM-AZI-3_2.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/MH-1/MH-1_1.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/MH-1/MH-1_2.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/MH-2/MH-2_1.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/MH-2/MH-2_2.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/MH-3/MH-3_1.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/MH-3/MH-3_2.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/MH-AZI-1/MH-AZI-1_1.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/MH-AZI-1/MH-AZI-1_2.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/MH-AZI-2/MH-AZI-2_1.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/MH-AZI-2/MH-AZI-2_2.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/MH-AZI-3/MH-AZI-3_1.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/MH-AZI-3/MH-AZI-3_2.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/Urine-1/Urine-1_1.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/Urine-1/Urine-1_2.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/Urine-2/Urine-2_1.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/Urine-2/Urine-2_2.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/Urine-3/Urine-3_1.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/Urine-3/Urine-3_2.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/Urine-AZI-1/Urine-AZI-1_1.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/Urine-AZI-1/Urine-AZI-1_2.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/Urine-AZI-2/Urine-AZI-2_1.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/Urine-AZI-2/Urine-AZI-2_2.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/Urine-AZI-3/Urine-AZI-3_1.fq.gz
    ./X101SC25062155-Z01-J002/01.RawData/Urine-AZI-3/Urine-AZI-3_2.fq.gz

Data_Tam_RNAseq_2025_LB-AB_IJ_W1_Y1_WT_vs_Mac-AB_IJ_W1_Y1_WT_on_ATCC19606/

    ./X101SC25015922-Z02-J002/01.RawData/LB-AB-1/LB-AB-1_1.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/LB-AB-1/LB-AB-1_2.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/LB-AB-2/LB-AB-2_1.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/LB-AB-2/LB-AB-2_2.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/LB-AB-3/LB-AB-3_1.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/LB-AB-3/LB-AB-3_2.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/LB-IJ-1/LB-IJ-1_1.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/LB-IJ-1/LB-IJ-1_2.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/LB-IJ-2/LB-IJ-2_1.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/LB-IJ-2/LB-IJ-2_2.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/LB-IJ-4/LB-IJ-4_1.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/LB-IJ-4/LB-IJ-4_2.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/LB-W1-1/LB-W1-1_1.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/LB-W1-1/LB-W1-1_2.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/LB-W1-2/LB-W1-2_1.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/LB-W1-2/LB-W1-2_2.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/LB-W1-3/LB-W1-3_1.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/LB-W1-3/LB-W1-3_2.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/LB-WT19606-2/LB-WT19606-2_1.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/LB-WT19606-2/LB-WT19606-2_2.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/LB-WT19606-3/LB-WT19606-3_1.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/LB-WT19606-3/LB-WT19606-3_2.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/LB-WT19606-4/LB-WT19606-4_1.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/LB-WT19606-4/LB-WT19606-4_2.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/LB-Y1-2/LB-Y1-2_1.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/LB-Y1-2/LB-Y1-2_2.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/LB-Y1-3/LB-Y1-3_1.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/LB-Y1-3/LB-Y1-3_2.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/LB-Y1-4/LB-Y1-4_1.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/LB-Y1-4/LB-Y1-4_2.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/Mac-AB-1/Mac-AB-1_1.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/Mac-AB-1/Mac-AB-1_2.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/Mac-AB-2/Mac-AB-2_1.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/Mac-AB-2/Mac-AB-2_2.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/Mac-AB-3/Mac-AB-3_1.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/Mac-AB-3/Mac-AB-3_2.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/Mac-IJ-1/Mac-IJ-1_1.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/Mac-IJ-1/Mac-IJ-1_2.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/Mac-IJ-2/Mac-IJ-2_1.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/Mac-IJ-2/Mac-IJ-2_2.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/Mac-IJ-4/Mac-IJ-4_1.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/Mac-IJ-4/Mac-IJ-4_2.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/Mac-W1-1/Mac-W1-1_1.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/Mac-W1-1/Mac-W1-1_2.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/Mac-W1-2/Mac-W1-2_1.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/Mac-W1-2/Mac-W1-2_2.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/Mac-W1-3/Mac-W1-3_1.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/Mac-W1-3/Mac-W1-3_2.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/Mac-WT19606-2/Mac-WT19606-2_1.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/Mac-WT19606-2/Mac-WT19606-2_2.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/Mac-WT19606-3/Mac-WT19606-3_1.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/Mac-WT19606-3/Mac-WT19606-3_2.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/Mac-WT19606-4/Mac-WT19606-4_1.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/Mac-WT19606-4/Mac-WT19606-4_2.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/Mac-Y1-2/Mac-Y1-2_1.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/Mac-Y1-2/Mac-Y1-2_2.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/Mac-Y1-3/Mac-Y1-3_1.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/Mac-Y1-3/Mac-Y1-3_2.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/Mac-Y1-4/Mac-Y1-4_1.fq.gz
    ./X101SC25015922-Z02-J002/01.RawData/Mac-Y1-4/Mac-Y1-4_2.fq.gz

Data_Tam_RNAseq_2025_subMIC_exposure_on_ATCC19606/

    ./X101SC25062155-Z01-J001/01.RawData/0_5ΔIJ-17-1/0_5ΔIJ-17-1_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/0_5ΔIJ-17-1/0_5ΔIJ-17-1_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/0_5ΔIJ-17-2/0_5ΔIJ-17-2_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/0_5ΔIJ-17-2/0_5ΔIJ-17-2_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/0_5ΔIJ-17-3/0_5ΔIJ-17-3_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/0_5ΔIJ-17-3/0_5ΔIJ-17-3_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/0_5ΔIJ-24-1/0_5ΔIJ-24-1_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/0_5ΔIJ-24-1/0_5ΔIJ-24-1_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/0_5ΔIJ-24-2/0_5ΔIJ-24-2_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/0_5ΔIJ-24-2/0_5ΔIJ-24-2_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/0_5ΔIJ-24-3/0_5ΔIJ-24-3_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/0_5ΔIJ-24-3/0_5ΔIJ-24-3_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/preWT-17-1/preWT-17-1_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/preWT-17-1/preWT-17-1_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/preWT-17-2/preWT-17-2_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/preWT-17-2/preWT-17-2_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/preWT-17-3/preWT-17-3_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/preWT-17-3/preWT-17-3_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/preWT-24-1/preWT-24-1_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/preWT-24-1/preWT-24-1_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/preWT-24-2/preWT-24-2_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/preWT-24-2/preWT-24-2_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/preWT-24-3/preWT-24-3_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/preWT-24-3/preWT-24-3_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/preΔIJ-17-1/preΔIJ-17-1_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/preΔIJ-17-1/preΔIJ-17-1_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/preΔIJ-17-2/preΔIJ-17-2_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/preΔIJ-17-2/preΔIJ-17-2_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/preΔIJ-17-3/preΔIJ-17-3_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/preΔIJ-17-3/preΔIJ-17-3_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/preΔIJ-24-1/preΔIJ-24-1_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/preΔIJ-24-1/preΔIJ-24-1_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/preΔIJ-24-2/preΔIJ-24-2_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/preΔIJ-24-2/preΔIJ-24-2_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/preΔIJ-24-3/preΔIJ-24-3_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/preΔIJ-24-3/preΔIJ-24-3_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/WT0_5-17-1/WT0_5-17-1_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/WT0_5-17-1/WT0_5-17-1_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/WT0_5-17-2/WT0_5-17-2_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/WT0_5-17-2/WT0_5-17-2_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/WT0_5-17-3/WT0_5-17-3_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/WT0_5-17-3/WT0_5-17-3_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/WT0_5-24-1/WT0_5-24-1_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/WT0_5-24-1/WT0_5-24-1_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/WT0_5-24-2/WT0_5-24-2_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/WT0_5-24-2/WT0_5-24-2_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/WT0_5-24-3/WT0_5-24-3_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/WT0_5-24-3/WT0_5-24-3_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/WT-17-1/WT-17-1_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/WT-17-1/WT-17-1_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/WT-17-2/WT-17-2_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/WT-17-2/WT-17-2_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/WT-17-3/WT-17-3_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/WT-17-3/WT-17-3_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/WT-24-1/WT-24-1_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/WT-24-1/WT-24-1_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/WT-24-2/WT-24-2_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/WT-24-2/WT-24-2_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/WT-24-3/WT-24-3_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/WT-24-3/WT-24-3_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/ΔIJ-17-1/ΔIJ-17-1_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/ΔIJ-17-1/ΔIJ-17-1_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/ΔIJ-17-2/ΔIJ-17-2_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/ΔIJ-17-2/ΔIJ-17-2_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/ΔIJ-17-3/ΔIJ-17-3_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/ΔIJ-17-3/ΔIJ-17-3_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/ΔIJ-24-1/ΔIJ-24-1_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/ΔIJ-24-1/ΔIJ-24-1_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/ΔIJ-24-2/ΔIJ-24-2_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/ΔIJ-24-2/ΔIJ-24-2_2.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/ΔIJ-24-3/ΔIJ-24-3_1.fq.gz
    ./X101SC25062155-Z01-J001/01.RawData/ΔIJ-24-3/ΔIJ-24-3_2.fq.gz

Data_Tam_DNAseq_2025_ATCC19606-Y1Y2Y3Y4W1W2W3W4/

    Illumina short-sequencing:

        ./X101SC24065637-Z01-J001/01.RawData/△adeIJ/△adeIJ_1.fq.gz
        ./X101SC24065637-Z01-J001/01.RawData/△adeIJ/△adeIJ_2.fq.gz
        ./X101SC24065637-Z01-J001/01.RawData/Tig1/Tig1_1.fq.gz
        ./X101SC24065637-Z01-J001/01.RawData/Tig1/Tig1_2.fq.gz
        ./X101SC24065637-Z01-J001/01.RawData/Tig2/Tig2_1.fq.gz
        ./X101SC24065637-Z01-J001/01.RawData/Tig2/Tig2_2.fq.gz
        ./X101SC24065637-Z01-J001/01.RawData/W/W_1.fq.gz
        ./X101SC24065637-Z01-J001/01.RawData/W/W_2.fq.gz
        ./X101SC24065637-Z01-J002/01.RawData/W2/W2_1.fq.gz
        ./X101SC24065637-Z01-J002/01.RawData/W2/W2_2.fq.gz
        ./X101SC24065637-Z01-J002/01.RawData/W3/W3_1.fq.gz
        ./X101SC24065637-Z01-J002/01.RawData/W3/W3_2.fq.gz
        ./X101SC24065637-Z01-J002/01.RawData/W4/W4_1.fq.gz
        ./X101SC24065637-Z01-J002/01.RawData/W4/W4_2.fq.gz
        ./X101SC24065637-Z01-J001/01.RawData/Y/Y_1.fq.gz
        ./X101SC24065637-Z01-J001/01.RawData/Y/Y_2.fq.gz
        ./X101SC24065637-Z01-J002/01.RawData/Y2/Y2_1.fq.gz
        ./X101SC24065637-Z01-J002/01.RawData/Y2/Y2_2.fq.gz
        ./X101SC24065637-Z01-J002/01.RawData/Y3/Y3_1.fq.gz
        ./X101SC24065637-Z01-J002/01.RawData/Y3/Y3_2.fq.gz
        ./X101SC24065637-Z01-J002/01.RawData/Y4/Y4_1.fq.gz
        ./X101SC24065637-Z01-J002/01.RawData/Y4/Y4_2.fq.gz

Nanopore long-sequencing:

        ./X101SC25080408-Z01-J001/Release-X101SC25080408-Z01-J001-20251009/Data-X101SC25080408-Z01-J001/W1/0710_2F_PBG50143_74807b09/W1_fastq_pass.tar
        ./X101SC25080408-Z01-J001/Release-X101SC25080408-Z01-J001-20251009/Data-X101SC25080408-Z01-J001/W1/0629_2H_PBG55359_f19e323f/W1_fastq_pass.tar
        ./X101SC25080408-Z01-J001/Release-X101SC25080408-Z01-J001-20251009/Data-X101SC25080408-Z01-J001/W1/0631_2C_PBG05153_55abe88b/W1_fastq_pass.tar
        ./X101SC25080408-Z01-J001/Release-X101SC25080408-Z01-J001-20251009/Data-X101SC25080408-Z01-J001/W2/0620_2C_PBG17000_6bfd0048/W2_fastq_pass.tar
        ./X101SC25080408-Z01-J001/Release-X101SC25080408-Z01-J001-20251009/Data-X101SC25080408-Z01-J001/W3/0710_2F_PBG50143_74807b09/W3_fastq_pass.tar
        ./X101SC25080408-Z01-J001/Release-X101SC25080408-Z01-J001-20251009/Data-X101SC25080408-Z01-J001/W3/0629_2H_PBG55359_f19e323f/W3_fastq_pass.tar
        ./X101SC25080408-Z01-J001/Release-X101SC25080408-Z01-J001-20251009/Data-X101SC25080408-Z01-J001/W4/0620_2C_PBG17000_6bfd0048/W4_fastq_pass.tar
        ./X101SC25080408-Z01-J001/Release-X101SC25080408-Z01-J001-20251009/Data-X101SC25080408-Z01-J001/Y1/0655_3B_PBE70655_6bbd09a4/Y1_fastq_pass.tar
        ./X101SC25080408-Z01-J001/Release-X101SC25080408-Z01-J001-20251009/Data-X101SC25080408-Z01-J001/Y1/0620_2C_PBG17000_6bfd0048/Y1_fastq_pass.tar
        ./X101SC25080408-Z01-J001/Release-X101SC25080408-Z01-J001-20251009/Data-X101SC25080408-Z01-J001/Y1/0631_2C_PBG05153_55abe88b/Y1_fastq_pass.tar
        ./X101SC25080408-Z01-J001/Release-X101SC25080408-Z01-J001-20251009/Data-X101SC25080408-Z01-J001/Y2/0620_2C_PBG17000_6bfd0048/Y2_fastq_pass.tar
        ./X101SC25080408-Z01-J001/Release-X101SC25080408-Z01-J001-20251009/Data-X101SC25080408-Z01-J001/Y3/0620_2C_PBG17000_6bfd0048/Y3_fastq_pass.tar
        ./X101SC25080408-Z01-J001/Release-X101SC25080408-Z01-J001-20251009/Data-X101SC25080408-Z01-J001/Y4/0620_2C_PBG17000_6bfd0048/Y4_fastq_pass.tar

Data_Tam_DNAseq_2025_AYE-WT_Q_S_craA-Tig4_craA-1-Cm200_craA-2-Cm200/

    ./X101SC25015922-Z01-J001/01.RawData/AYE-craA-1onCm200/AYE-craA-1onCm200_1.fq.gz
    ./X101SC25015922-Z01-J001/01.RawData/AYE-craA-1onCm200/AYE-craA-1onCm200_2.fq.gz
    ./X101SC25015922-Z01-J001/01.RawData/AYE-craA-2onCm200/AYE-craA-2onCm200_1.fq.gz
    ./X101SC25015922-Z01-J001/01.RawData/AYE-craA-2onCm200/AYE-craA-2onCm200_2.fq.gz
    ./X101SC25015922-Z01-J001/01.RawData/AYE-craAonTig4/AYE-craAonTig4_1.fq.gz
    ./X101SC25015922-Z01-J001/01.RawData/AYE-craAonTig4/AYE-craAonTig4_2.fq.gz
    ./X101SC25015922-Z01-J001/01.RawData/AYE-Q/AYE-Q_1.fq.gz
    ./X101SC25015922-Z01-J001/01.RawData/AYE-Q/AYE-Q_2.fq.gz
    ./X101SC25015922-Z01-J001/01.RawData/AYE-S/AYE-S_1.fq.gz
    ./X101SC25015922-Z01-J001/01.RawData/AYE-S/AYE-S_2.fq.gz
    ./X101SC25015922-Z01-J001/01.RawData/AYE-WTonTig4/AYE-WTonTig4_1.fq.gz
    ./X101SC25015922-Z01-J001/01.RawData/AYE-WTonTig4/AYE-WTonTig4_2.fq.gz
    ./X101SC25015922-Z01-J001/01.RawData/clinical/clinical_1.fq.gz
    ./X101SC25015922-Z01-J001/01.RawData/clinical/clinical_2.fq.gz

Data_Tam_DNAseq_2025_E.hormaechei-adeABadeIJ_adeIJK_CM1_CM2

    ./X101SC24115801-Z01-J001/01.RawData/adeABadeIJ/adeABadeIJ_1.fq.gz
    ./X101SC24115801-Z01-J001/01.RawData/adeABadeIJ/adeABadeIJ_2.fq.gz
    ./X101SC24115801-Z01-J001/01.RawData/adeIJK/adeIJK_1.fq.gz
    ./X101SC24115801-Z01-J001/01.RawData/adeIJK/adeIJK_2.fq.gz
    ./X101SC24115801-Z01-J001/01.RawData/CM1/CM1_1.fq.gz
    ./X101SC24115801-Z01-J001/01.RawData/CM1/CM1_2.fq.gz
    ./X101SC24115801-Z01-J001/01.RawData/CM2/CM2_1.fq.gz
    ./X101SC24115801-Z01-J001/01.RawData/CM2/CM2_2.fq.gz
    ./X101SC24115801-Z01-J001/01.RawData/HF/HF_1.fq.gz
    ./X101SC24115801-Z01-J001/01.RawData/HF/HF_2.fq.gz

Data_Tam_DNAseq_2026_19606deltaIJfluE/

    ./X101SC25116512-Z01-J003/01.RawData/19606△ABfluEcef-1/19606△ABfluEcef-1_1.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606△ABfluEcef-1/19606△ABfluEcef-1_2.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606△ABfluEcipro-2/19606△ABfluEcipro-2_1.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606△ABfluEcipro-2/19606△ABfluEcipro-2_2.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606△ABfluEdori-2/19606△ABfluEdori-2_1.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606△ABfluEdori-2/19606△ABfluEdori-2_2.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606△ABfluEnitro-3/19606△ABfluEnitro-3_1.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606△ABfluEnitro-3/19606△ABfluEnitro-3_2.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606△ABfluEpip-1/19606△ABfluEpip-1_1.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606△ABfluEpip-1/19606△ABfluEpip-1_2.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606△ABfluEpolyB-3/19606△ABfluEpolyB-3_1.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606△ABfluEpolyB-3/19606△ABfluEpolyB-3_2.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606△ABfluEtet-1/19606△ABfluEtet-1_1.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606△ABfluEtet-1/19606△ABfluEtet-1_2.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606△IJfluEcef-4/19606△IJfluEcef-4_1.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606△IJfluEcef-4/19606△IJfluEcef-4_2.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606△IJfluEcipro-3/19606△IJfluEcipro-3_1.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606△IJfluEcipro-3/19606△IJfluEcipro-3_2.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606△IJfluEdori-1/19606△IJfluEdori-1_1.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606△IJfluEdori-1/19606△IJfluEdori-1_2.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606△IJfluEnitro-3/19606△IJfluEnitro-3_1.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606△IJfluEnitro-3/19606△IJfluEnitro-3_2.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606△IJfluEpip-4/19606△IJfluEpip-4_1.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606△IJfluEpip-4/19606△IJfluEpip-4_2.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606△IJfluEpolyB-4/19606△IJfluEpolyB-4_1.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606△IJfluEpolyB-4/19606△IJfluEpolyB-4_2.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606wtfluEcef-1/19606wtfluEcef-1_1.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606wtfluEcef-1/19606wtfluEcef-1_2.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606wtfluEcipro-2/19606wtfluEcipro-2_1.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606wtfluEcipro-2/19606wtfluEcipro-2_2.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606wtfluEdori-1/19606wtfluEdori-1_1.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606wtfluEdori-1/19606wtfluEdori-1_2.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606wtfluEnitro-1/19606wtfluEnitro-1_1.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606wtfluEnitro-1/19606wtfluEnitro-1_2.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606wtfluEpip-4/19606wtfluEpip-4_1.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606wtfluEpip-4/19606wtfluEpip-4_2.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606wtfluEpolyB-4/19606wtfluEpolyB-4_1.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606wtfluEpolyB-4/19606wtfluEpolyB-4_2.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606wtfluEtet-2/19606wtfluEtet-2_1.fq.gz
    ./X101SC25116512-Z01-J003/01.RawData/19606wtfluEtet-2/19606wtfluEtet-2_2.fq.gz

Data_Tam_DNAseq_2026_Acinetobacter_harbinensis/

    ./X101SC25116512-Z01-J002/01.RawData/An6/An6_1.fq.gz
    ./X101SC25116512-Z01-J002/01.RawData/An6/An6_2.fq.gz

Data_Tam_Metagenomics_2026/

    ./X101SC25123808-Z01-J001/01.RawData/A1/A1_1.fq.gz
    ./X101SC25123808-Z01-J001/01.RawData/A1/A1_2.fq.gz
    ./X101SC25123808-Z01-J001/01.RawData/A1a/A1a_1.fq.gz
    ./X101SC25123808-Z01-J001/01.RawData/A1a/A1a_2.fq.gz
    ./X101SC25123808-Z01-J001/01.RawData/A2/A2_1.fq.gz
    ./X101SC25123808-Z01-J001/01.RawData/A2/A2_2.fq.gz
    ./X101SC25123808-Z01-J001/01.RawData/B1/B1_1.fq.gz
    ./X101SC25123808-Z01-J001/01.RawData/B1/B1_2.fq.gz
    ./X101SC25123808-Z01-J001/01.RawData/B2/B2_1.fq.gz
    ./X101SC25123808-Z01-J001/01.RawData/B2/B2_2.fq.gz

Data_Foong_RNAseq_2021_ATCC19606_Cm/

    wt_r1_R1.fq.gz -> ../raw_data_batch1/WT_1_1.fq.gz
    wt_r1_R2.fq.gz -> ../raw_data_batch1/WT_1_2.fq.gz
    wt_r2_R1.fq.gz -> ../raw_data_batch1/WT_2B_1.fq.gz
    wt_r2_R2.fq.gz -> ../raw_data_batch1/WT_2B_2.fq.gz
    craA_r1_R1.fq.gz -> ../raw_data_batch1/C_1B_1.fq.gz
    craA_r1_R2.fq.gz -> ../raw_data_batch1/C_1B_2.fq.gz
    craA_r2_R1.fq.gz -> ../raw_data_batch1/C_2_1.fq.gz
    craA_r2_R2.fq.gz -> ../raw_data_batch1/C_2_2.fq.gz
    adeIJ_r1_R1.fq.gz -> ../raw_data_batch1/J_1_1.fq.gz
    adeIJ_r1_R2.fq.gz -> ../raw_data_batch1/J_1_2.fq.gz
    adeIJ_r2_R1.fq.gz -> ../raw_data_batch1/J_2_1.fq.gz
    adeIJ_r2_R2.fq.gz -> ../raw_data_batch1/J_2_2.fq.gz
    wt_r3_R1.fq.gz -> ../raw_data_batch2/Control_1.fq.gz
    wt_r3_R2.fq.gz -> ../raw_data_batch2/Control_2.fq.gz
    wt.abx_r1_R1.fq.gz -> ../raw_data_batch2/WT_1B_1.fq.gz
    wt.abx_r1_R2.fq.gz -> ../raw_data_batch2/WT_1B_2.fq.gz
    wt.abx_r2_R1.fq.gz -> ../raw_data_batch2/WT_2B_1.fq.gz
    wt.abx_r2_R2.fq.gz -> ../raw_data_batch2/WT_2B_2.fq.gz
    wt.abx_r3_R1.fq.gz -> ../raw_data_batch2/WT_3B_1.fq.gz
    wt.abx_r3_R2.fq.gz -> ../raw_data_batch2/WT_3B_2.fq.gz
    craA.abx_r1_R1.fq.gz -> ../raw_data_batch2/Cra_1_1.fq.gz
    craA.abx_r1_R2.fq.gz -> ../raw_data_batch2/Cra_1_2.fq.gz
    craA.abx_r2_R1.fq.gz -> ../raw_data_batch2/Cra_2_1.fq.gz
    craA.abx_r2_R2.fq.gz -> ../raw_data_batch2/Cra_2_2.fq.gz
    craA.abx_r3_R1.fq.gz -> ../raw_data_batch2/Cra_3_1.fq.gz
    craA.abx_r3_R2.fq.gz -> ../raw_data_batch2/Cra_3_2.fq.gz
    adeIJ.abx_r1_R1.fq.gz -> ../raw_data_batch2/IJ_1B_1.fq.gz
    adeIJ.abx_r1_R2.fq.gz -> ../raw_data_batch2/IJ_1B_2.fq.gz
    adeIJ.abx_r2_R1.fq.gz -> ../raw_data_batch2/IJ_2B_1.fq.gz
    adeIJ.abx_r2_R2.fq.gz -> ../raw_data_batch2/IJ_2B_2.fq.gz
    adeIJ.abx_r3_R1.fq.gz -> ../raw_data_batch2/IJ_3_1.fq.gz
    adeIJ.abx_r3_R2.fq.gz -> ../raw_data_batch2/IJ_3_2.fq.gz
    adeIJ_r3_R1.fq.gz -> ../raw_data_batch3/adIJ_1_1.fq.gz
    adeIJ_r3_R2.fq.gz -> ../raw_data_batch3/adIJ_1_2.fq.gz
    adeIJ_r4_R1.fq.gz -> ../raw_data_batch3/adIJ_2_1.fq.gz
    adeIJ_r4_R2.fq.gz -> ../raw_data_batch3/adIJ_2_2.fq.gz
    craA_r3_R1.fq.gz -> ../raw_data_batch3/crA2_1.fq.gz
    craA_r3_R2.fq.gz -> ../raw_data_batch3/crA2_2.fq.gz
    craA.abx_r4_R1.fq.gz -> ../raw_data_batch3/crA_ab_1_1.fq.gz
    craA.abx_r4_R2.fq.gz -> ../raw_data_batch3/crA_ab_1_2.fq.gz
    craA.abx_r5_R1.fq.gz -> ../raw_data_batch3/crA_ab_2_1.fq.gz
    craA.abx_r5_R2.fq.gz -> ../raw_data_batch3/crA_ab_2_2.fq.gz
    craA.abx_r6_R1.fq.gz -> ../raw_data_batch3/crA_ab_3_1.fq.gz
    craA.abx_r6_R2.fq.gz -> ../raw_data_batch3/crA_ab_3_2.fq.gz
    adeAB_r1_R1.fq.gz -> ../raw_data_batch3/adAB_1_1.fq.gz
    adeAB_r1_R2.fq.gz -> ../raw_data_batch3/adAB_1_2.fq.gz
    adeAB_r2_R1.fq.gz -> ../raw_data_batch3/adAB_2_1.fq.gz
    adeAB_r2_R2.fq.gz -> ../raw_data_batch3/adAB_2_2.fq.gz
    adeAB.abx_r1_R1.fq.gz -> ../raw_data_batch3/adAB_ab1_1.fq.gz
    adeAB.abx_r1_R2.fq.gz -> ../raw_data_batch3/adAB_ab1_2.fq.gz
    adeAB.abx_r2_R1.fq.gz -> ../raw_data_batch3/adAB_ab2_1.fq.gz
    adeAB.abx_r2_R2.fq.gz -> ../raw_data_batch3/adAB_ab2_2.fq.gz
    adeAB.abx_r3_R1.fq.gz -> ../raw_data_batch3/adAB_ab3_1.fq.gz
    adeAB.abx_r3_R2.fq.gz -> ../raw_data_batch3/adAB_ab3_2.fq.gz

Data_Foong_DNAseq_2025_AYE_Dark_vs_Light/

    ./X101SC25116512-Z01-J001/01.RawData/Dark/Dark_1.fq.gz
    ./X101SC25116512-Z01-J001/01.RawData/Dark/Dark_2.fq.gz
    ./X101SC25116512-Z01-J001/01.RawData/Light/Light_1.fq.gz
    ./X101SC25116512-Z01-J001/01.RawData/Light/Light_2.fq.gz

Directory Listings Summary

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/media/jhuang/INTENSO

(empty; data now on ~/DATA_Intenso)

#	Name
1	(empty)

~/DATA

#	Name
1	Data_Ute_MKL1
2	Data_Ute_RNA_4_2022-11_test
3	Data_Ute_RNA_3
4	Data_Susanne_Carotis_RNASeq_PUBLISHING
5	Data_Jiline_Yersinia_SNP
6	Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex_DUPLICATED_DEL
7	Data_Nicole_CRC1648
8	Mouse_HS3ST1_12373_out
9	Mouse_HS3ST1_12175_out
10	Data_Biobakery
11	Data_Xiaobo_10x_2
12	Data_Xiaobo_10x_3
13	Talk_Nicole_CRC1648
14	Talks_Bioinformatics_Meeting
15	Talks_resources
16	Data_Susanne_MPox_DAMIAN
17	Data_host_transcriptional_response
18	Talks_including_DEEP-DV
19	DOKTORARBEIT
20	Data_Susanne_MPox
21	Data_Jiline_Transposon
22	Data_Jiline_Transposon2
23	Data_Matlab
24	deepseek-ai
25	Stick_Mi_DEL
26	TODO_shares
27	Data_Ute_RNA_4
28	Data_Liu_PCA_plot
29	README_run_viral-ngs_inside_Docker
30	README_compare_genomes
31	mapped.bam
32	Data_Serpapi
33	Data_Ute_RNA_1_2
34	Data_Marc_RNAseq_2024
35	Data_Nicole_CaptureProbeSequencing
36	LOG_mapping
37	Data_Huang_Human_herpesvirus_3
38	Data_Nicole_DAMIAN_Post-processing_Pathoprobe_FluB_Links
39	Access_to_Win7
40	Data_DAMIAN_Post-processing_Flavivirus_and_FSME_and_Haemophilus
41	Data_Luise_Sepi_STKN
42	Data_Patricia_Sepi_7samples
43	Data_Soeren_2025_PUBLISHING
44	Data_Ben_RNAseq_2025
45	Data_Tam_DNAseq_2025_AYE-WT_Q_S_craA-Tig4_craA-1-Cm200_craA-2-Cm200
46	Data_Patricia_Transposon
47	Data_Patricia_Transposon_2025
48	Colocation_Space
49	Data_Tam_Methylation_2025_empty
50	2025-11-03_eVB-Schreiben_12-57.pdf
51	DEGs_Group1_A1-A3+A8-A10_vs_Group2_B10-B16.png
52	README.pdf
53	Data_Hannes_JCM00612
54	167_redundant_DEL
55	Lehre_Bioinformatik
56	Data_Ben_Boruta_Analysis
57	Data_Childrensclinic_16S_2025_DEL
58	Data_Ben_Mycobacterium_pseudoscrofulaceum
59	Foong_RNA_mSystems_Huang_Changed.txt
60	Data_Pietro_Scatturo_and_Charlotte_Uetrecht_16S_2025
61	Data_JuliaBerger_RNASeq_SARS-CoV-2
62	Data_PaulBongarts_S.epidermidis_HDRNA
63	Data_Ute
64	Data_Foong_DNAseq_2025_AYE_Dark_vs_Light_TODO
65	Data_Foong_RNAseq_2021_ATCC19606_Cm
66	Data_Tam_Funding
67	Data_Tam_RNAseq_2025_LB-AB_IJ_W1_Y1_WT_vs_Mac-AB_IJ_W1_Y1_WT_on_ATCC19606
68	Data_Tam_RNAseq_2025_subMIC_exposure_on_ATCC19606
69	Data_Tam.txt
70	Data_Tam_RNAseq_2024_AUM_MHB_Urine_on_ATCC19606
71	Data_Tam_Metagenomics_2026
72	Data_Michelle
73	Data_Nicole_16S_2025_Childrensclinic
74	Data_Sophie_HDV_Sequences
75	Data_Tam_DNAseq_2026_19606deltaIJfluE
76	README_nf-core
77	Data_Vero_Kymographs
78	Access_to_Win10
79	Data_Patricia_AMRFinderPlus_2025
80	Data_Tam_DNAseq_2025_Unknown-adeABadeIJ_adeIJK_CM1_CM2
81	Data_Damian
82	Data_Karoline_16S
83	Data_JuliaFuchs_RNAseq_2025
84	Data_Tam_DNAseq_2025_ATCC19606-Y1Y2Y3Y4W1W2W3W4_TODO
85	Data_Tam_DNAseq_2026_Acinetobacter_harbinensis
86	Data_Benjamin_DNAseq_2026_GE11174
87	Data_Susanne_spatialRNA_2022.9.1_backup
88	Data_Susanne_spatialRNA

~/DATA_A

#	Name
1	Data_Damian_NEW_CREATED
2	Data_R_bubbleplots
3	Data_Ute_TRANSFERED_DEL
4	Paper_Target_capture_sequencing_MHH_PUBLISHED
5	Data_Nicole8_Lamprecht_new_PUBLISHED
6	Data_Samira_RNAseq

~/DATA_B

#	Name
1	Data_DAMIAN_endocarditis_encephalitis
2	Data_Denise_sT_PUBLISHING
3	Data_Fran2_16S_func
4	Data_Holger_5179-R1_vs_5179
5	Antraege_
6	Data_16S_Nicole_210222
7	Data_Adam_Influenza_A_virus
8	Data_Anna_Efaecium_assembly
9	Data_Bactopia
10	Data_Ben_RNAseq
11	Data_Johannes_PIV3
12	Data_Luise_Epidome_longitudinal_nose
13	Data_Manja_Hannes_Probedesign
14	Data_Marc_AD_PUBLISHING
15	Data_Marc_RNA-seq_Saureus_Review
16	Data_Nicole_16S
17	Data_Nicole_cfDNA_pathogens
18	Data_Ring_and_CSF_PegivirusC_DAMIAN
19	Data_Song_Microarray
20	Data_Susanne_Omnikron
21	Data_Viro
22	Doktorarbeit
23	Poster_Rohde_20230724
24	Data_Django
25	Data_Holger_S.epidermidis_1585_5179_HD05
26	Data_Manja_RNAseq_Organoids_Virus
27	Data_Holger_MT880870_MT880872_Annotation
28	Data_Soeren_RNA-seq_2022
29	Data_Manja_RNAseq_Organoids_Merged
30	Data_Gunnar_Yersiniomics
31	Data_Manja_RNAseq_Organoids
32	Data_Susanne_Carotis_MS

~/DATA_C

(names only; as listed)

#	Name
1	2022-10-27_IRI_manuscript_v03_JH.docx
2	16304905.fasta
3	’16S data manuscript_NF.docx’
4	180820_2_supp_4265595_sw6zjk.docx
5	180820_2_supp_4265596_sw6zjk.docx
6	1a_vs_3.csv
7	‘2.05.01.05-A01 Urlaubsantrag-Shuting-beantragt.pdf’
8	2014SawickaBBA.pdf
9	20160509Manuscript_NDM_OXA_mitKomm.doc
10	220607_Agenda_monthly_meeting.pdf
11	‘20221129 Table mutations.docx’
12	230602_NB501882_0428_AHKG53BGXT.zip
13	362383173.rar
14	562.9459.1.fa
15	562.9459.1_rc.fa
16	ASA3P.pdf
17	All_indels_annotated_vHR.xlsx
18	‘Amplikon_indeces_Susanne +groups.xlsx’
19	Amplikon_indeces_Susanne.xlsx
20	GAMOLA2
21	Data_Susanne_Carotis_spatialRNA_PUBLISHING (dead link)
22	Data_Paul_Staphylococcus_epidermidis
23	Data_Nicola_Schaltenberg_PICRUSt
24	Data_Nicola_Schaltenberg
25	Data_Nicola_Gagliani
26	Data_methylome_MMc
27	Data_Jingang
28	Data_Indra_RNASeq_GSM2262901
29	Data_Holger_VRE
30	Data_Holger_Pseudomonas_aeruginosa_SNP
31	Data_Hannes_ChIPSeq
32	Data_Emilia_MeDIP
33	Data_ChristophFR_HepE_published
34	Data_Christopher_MeDIP_MMc_published
35	Data_Anna_Kieler_Sepi_Staemme
36	Data_Anna12_HAPDICS_final
37	Data_Anastasia_RNASeq_PUBLISHING
38	Aufnahmeantrag_komplett_10_2022.pdf
39	Astrovirus.pdf
40	COMMANDS
41	Bacterial_pipelines.txt
42	COMPSRA_uke_DEL.jar
43	ChIPSeq_pipeline_desc.docx
44	ChIPSeq_pipeline_desc.pdf
45	Comparative_genomic_analysis_of_eight_novel_haloal.pdf
46	CvO_Klassenliste_7_3.pdf
47	‘Copy of pool_b1_CGATGT_300.xlsx’
48	Fran_16S_Exp8-17-21-27.txt
49	HPI_DRIVE
50	HEV_aligned.fasta
51	INTENSO_DIR
52	HPI_samples_for_NGS_29.09.22.xlsx
53	Hotmail_to_Gmail
54	Indra_Thesis_161020.pdf
55	‘LT K331A.gbk’
56	LOG_p954_stat
57	LOG
58	Manuscript_10_02_2021.docx
59	Metagenomics_Tools_and_Insights.pdf
60	‘Miseq Amplikon LAuf April.xlsx’
61	NGS.tar.gz
62	Nachweis_Bakterien_Viren_im_Hochdurchsatz.pdf
63	Nicole8_Lamprecht_logs
64	Nanopore.handouts.pdf
65	‘Norovirus paper Susanne 191105.docx’
66	PhyloRNAalifold.pdf
67	README_R
68	README_RNAHiSwitch_DEL
69	RNA-NGS_Analysis_modul3_NanoStringNorm.zip
70	RNAConSLOptV1.2.tar.gz
71	‘RSV GFP5 including 3`UTR.docx’
72	SNPs_on_pangenome.txt
73	SERVER
74	R_tutorials-master.zip
75	Rawdata_Readme.pdf
76	SUB10826945_record_preview.txt
77	S_staphylococcus_annotated_diff_expr.xls
78	Snakefile_list
79	Source_Classification_Code.rds
80	Supplementary_Table_S3.xlsx
81	Untitled.ipynb
82	UniproUGENE_UserManual.pdf
83	Untitled1.ipynb
84	Untitled2.ipynb
85	Untitled3.ipynb
86	WAC6h_vs_WAP6h_down.txt
87	damian_nodbs
88	WAC6h_vs_WAP6h_up.txt
89	‘add. Figures Hamburg_UKE.pptx’
90	all_gene_counts_with_annotation.xlsx
91	app_flask.py
92	bengal-bay-0.1.json
93	bengal3_ac3.yml
94	call_shell_from_Ruby.png
95	bengal3ac3.yml
96	empty.fasta
97	coefficients_csaw_vs_diffreps.xlsx
98	exchange.txt
99	exdata-data-NEI_data.zip
100	genes_wac6_wap6.xls
101	go1.13.linux-amd64.tar.gz.1
102	hev_p2-p5.fa
103	map_corrected_backup.txt
104	install_nginx_on_hamm
105	hg19.rmsk.bed
106	metadata-9563675-processed-ok.tsv
107	mkg_sprechstundenflyer_ver1b_dezember_2019.pdf
108	multiqc_config.yaml
109	p11326_OMIKRON3398_corsurv.gb
110	p11326_OMIKRON3398_corsurv.gb_converted.fna
111	parseGenbank_reformat.py
112	pangenome-snakemake-master.zip
113	‘phylo tree draft.pdf’
114	qiime_params.txt
115	pool_b1_CGATGT_300.zip
116	qiime_params_backup.txt
117	qiime_params_s16_s18.txt
118	snakePipes
119	results_description.html
120	rnaalihishapes.tar.gz
121	rnaseq_length_bias.pdf
122	3932-Leber
123	BioPython
124	Biopython
125	DEEP-DV
126	DOKTORARBEIT
127	Data_16S_Arck_vaginal_stool
128	Data_16S_BS052
129	Data_16S_Birgit
130	Data_16S_Christner
131	Data_16S_Leonie
132	Data_16S_PatientA-G_CSF
133	Data_16S_Schaltenberg
134	Data_16S_benchmark
135	Data_16S_benchmark2
136	Data_16S_gcdh_BKV
137	Data_Alex1_Amplicon
138	Data_Alex1_SNP
139	Data_Analysis_for_Life_Science
140	Data_Anna13_vanA-Element
141	Data_Anna14_PACBIO_methylation
142	Data_Anna_C.acnes2_old_DEL
143	Data_Anna_MT880872_update
144	Data_Anna_gap_filling_agrC
145	Data_Baechlein_Hepacivirus_2018
146	Data_Bornavirus
147	Data_CSF
148	Data_Christine_cz19-178-rothirsch-bovines-hepacivirus
149	Data_Daniela_adenovirus_WGS
150	Data_Emilia_MeDIP_DEL
151	Data_Francesco2021_16S
152	Data_Francesco2021_16S_re
153	Data_Gunnar_MS
154	Data_Hannes_RNASeq
155	Data_Holger_Efaecium_variants_PUBLISHED
156	Data_Holger_VRE_DEL
157	Data_Icebear_Damian
158	Data_Indra3_H3K4_p2_DEL
159	Data_Indra6_RNASeq_ChipSeq_Integration_DEL
160	Data_Indra_Figures
161	Data_KatjaGiersch_new_HDV
162	Data_MHH_Encephalitits_DAMIAN
163	Data_Manja_RPAChIPSeq_public
164	Data_Manuel_WGS_Yersinia
165	Data_Manuel_WGS_Yersinia2_DEL
166	Data_Manuel_WGS_Yersinia_DEL
167	Data_Marcus_tracrRNA_structures
168	Data_Mausmaki_Damian
169	Data_Nicole1_Tropheryma_whipplei
170	Data_Nicole5
171	Data_Nicole5_77-92
172	Data_PaulBecher_Rotavirus
173	Data_Pietschmann_HCV_Amplicon_bigFile
174	Data_Piscine_Orthoreovirus_3_in_Brown_Trout
175	Data_Proteomics
176	Data_RNABioinformatics
177	Data_RNAKinetics
178	Data_R_courses
179	Data_SARS-CoV-2
180	Data_SARS-CoV-2_Genome_Announcement_PUBLISHED
181	Data_Seite
182	Data_Song_aggregate_sum
183	Data_Susanne_Amplicon_RdRp_orf1_2_re
184	Data_Tabea_RNASeq
185	Data_Thaiss1_Microarray_new
186	Data_Tintelnot_16S
187	Data_Wuenee_Plots
188	Data_Yang_Poster
189	Data_jupnote
190	Data_parainfluenza
191	Data_snakemake_recipe
192	Data_temp
193	Data_viGEN
194	Genomic_Data_Science
195	Learn_UGENE
196	MMcPaper
197	Manuscript_Epigenetics_Macrophage_Yersinia
198	Manuscript_RNAHiSwitch
199	MeDIP_Emilia_copy_DEL
200	Method_biopython
201	NGS
202	Okazaki-Seq_Processing
203	RNA-NGS_Analysis_modul3_NanoStringNorm
204	RNAConSLOptV1.2
205	RNAHeliCes
206	RNA_li_HeliCes
207	RNAliHeliCes
208	RNAliHeliCes_Relatedshapes_modified
209	R_refcard
210	R_DataCamp
211	R_cats_package
212	R_tutorials-master
213	SnakeChunks
214	align_4l_on_FJ705359
215	align_4p_on_FJ705359
216	assembly
217	bacto
218	bam2fastq_mapping_again
219	chipster
220	damian_GUI
221	enhancer-snakemake-demo
222	hg19_gene_annotations
223	interlab_comparison_DEL
224	my_flask
225	papers
226	pangenome-snakemake_zhaoc1
227	pyflow-epilogos
228	raw_data_rnaseq_Indra
229	test_raw_data_dnaseq
230	test_raw_data_rnaseq
231	to_Francesco
232	ukepipe
233	ukepipe_nf
234	var_www_DjangoApp_mysite2_2023-05
235	roentgenpass.pdf
236	salmon_tx2gene_GRCh38.tsv
237	salmon_tx2gene_chrHsv1.tsv
238	‘sample IDs_Lamprecht.xlsx’
239	summarySCC_PM25.rds
240	untitled.py
241	tutorial-rnaseq.pdf
242	x.log
243	webapp.tar.gz
244	temp
245	temp2
246	Data_Susanne_Amplicon_haplotype_analyses_RdRp_orf1_2_re
247	Data_Susanne_WGS_unbiased

~/DATA_D

#	Name
1	Data_Soeren_RNA-seq_2023_PUBLISHING
2	Data_Ute
3	Data_Marc_RNA-seq_Sepidermidis
4	Data_Patricia_Transposon
5	Books_DA_for_Life
6	Data_Sven
7	Datasize_calculation_based_on_coverage.txt
8	Data_Paul_HD46_1-wt_resequencing
9	Data_Sanam_DAMIAN
10	Data_Tam_variant_calling
11	Data_Samira_Manuscripts
12	Data_Silvia_VoltRon_Debug
13	Data_Pietschmann_229ECoronavirus_Mutations_2024
14	Data_Pietschmann_229ECoronavirus_Mutations_2025
15	Data_Birthe_Svenja_RSV_Probe3_PUBLISHING

~/DATA_E

#	Name
1	j_huang_until_201904
2	Data_2019_April
3	Data_2019_May
4	Data_2019_June
5	Data_2019_July
6	Data_2019_August
7	Data_2019_September
8	Data_Song_RNASeq_PUBLISHED
9	Data_Laura_MP_RNASeq
10	Data_Nicole6_HEV_Swantje2
11	Data_Becher_Damian_Picornavirus_BovHepV
12	bacteria_refseq.zip
13	bacteria_refseq
14	Data_Rotavirus
15	Data_Xiaobo_10x
16	Data_Becher_Damian_Picornavirus_BovHepV_INCOMPLETE_DEL

~/DATA_Intenso

#	Name
1	HOME_FREIBURG_DEL
2	150810_M03701_0019_000000000-AFJFK
3	Data_Thaiss2_Microarray
4	VirtualBox_VMs_DEL
5	‘VirtualBox VMs_DEL’
6	‘VirtualBox VMs2_DEL’
7	websites
8	DATA
9	Data_Laura
10	Data_Laura_2
11	Data_Laura_3
12	galaxy_tools
13	Downloads2
14	Downloads
15	mom-baby_com_cn
16	‘VirtualBox VMs2’
17	VirtualBox_VMs
18	CLC_Data
19	Work_Dir2
20	Work_Dir2_SGE
21	Data_SPANDx1_Kpneumoniae_vs_Assembly1
22	MauveOutput
23	Fastqs
24	Data_Anna3_VRE_Ausbruch
25	Work_Dir_mock_broad_mockinput
26	Work_Dir_dM_broad_mockinput
27	Data_Anna8_RNASeq_static_shake_deprecated
28	PENDRIVE_cont
29	Work_Dir_WAP_broad_mockinput
30	Work_Dir_WAC_broad_mockinput
31	Work_Dir_dP_broad_mockinput
32	Data_Nicole10_16S_interlab
33	PAPERS
34	TB
35	Data_Anna4_SNP
36	Data_Carolin1_16S
37	ChipSeq_Raw_Data3_171009_NB501882_0024_AHNGTYBGX3
38	m_aepfelbacher_DEL.zip
39	Data_Anna7_RNASeq_Cytoscape
40	Data_Nicole9_Hund_Katze_Mega
41	Data_Anna2_CO6114
42	Data_Nicole3_TH17_orig
43	Data_Nicole1_Tropheryma_whipplei
44	results_K27
45	‘VirtualBox VMs’
46	Data_Anna6_RNASeq
47	Data_Anna1_1585_RNAseq
48	Data_Thaiss1_Microarray
49	Data_Nicole7_Anelloviruses_Polyomavirus
50	Data_Nina1_Nicole5_1-76
51	Data_Nina1_merged
52	Data_Nicole8_Lamprecht
53	Data_Anna5_SNP
54	chipseq
55	Downloads_DEL
56	Data_Gagliani2_enriched_16S
57	Data_Gagliani1_18S_16S
58	m_aepfelbacher
59	Data_Susanne_WGS_3amplicons

/media/jhuang/Titisee

#	Name
1	Data_Anna4_SNP
2	Data_Anna5_SNP_rsync_error
3	TRASH
4	Data_Nicole6_HEV_4_SNP_calling_PE_DEL
5	Data_Nina1_Nicole7
6	Data_Nicole6_HEV_4_SNP_calling_SE_DEL
7	180119_M03701_0115_000000000-BFG46.zip
8	Data_Nicole10_16S_interlab_PUBLISHED
9	Anna11_assemblies
10	Anna11_trees
11	Data_Nicole6_HEV_new_orig_fastqs
12	Data_Anna9_OXA-48_or_OXA-181
13	bengal_results_v1_2018
14	DO.pdf
15	damian_DEL
16	MAGpy_db
17	UGENE_v1_32_data_cistrome
18	UGENE_v1_32_data_ngs_classification
19	Data_Nicole6_HEV_Swantje
20	Data_Nico_Gagliani
21	GAMOLA2_prototyp
22	Thomas_methylation_EPIC_DO
23	Data_Nicola_Schaltenberg
24	Data_Nicola_Schaltenberg_PICRUSt
25	HOME_FREIBURG
26	Data_Francesco_16S
27	3rd_party
28	ConsPred_prokaryotic_genome_annotation
29	‘System Volume Information’
30	damian_v201016
31	Data_Holger_VRE
32	Data_Holger_Pseudomonas_aeruginosa_SNP
33	Eigene_Ordner_HR
34	GAMOLA2
35	Data_Anastasia_RNASeq
36	Data_Amir_PUBLISHED
37	‘$RECYCLE.BIN’
38	Data_Xiaobo_10x_3
39	Data_Tam_DNAseq_2023_Comparative_ATCC19606_AYE_ATCC17978
40	Data_Holger_S.epidermidis_short
41	TEMP
42	Data_Holger_S.epidermidis_long

/media/jhuang/Elements(Denise_ChIPseq)

#	Name
1	Data_Denise_LTtrunc_H3K27me3_2_results_DEL
2	Data_Denise_LTtrunc_H3K4me3_2_results_DEL
3	Data_Anna12_HAPDICS_final_not_finished_DEL
4	m_aepfelbacher_DEL
5	Data_Damian
6	ST772_DEL
7	ALL_trimmed_part_DEL
8	Data_Denise_ChIPSeq_Protocol1
9	Data_Pietschmann_HCV_Amplicon
10	Data_Nicole6_HEV_ownMethod_new
11	HD04-1.fasta
12	RNAHiSwitch_
13	RNAHiSwitch__
14	RNAHiSwitch___
15	RNAHiSwitchpaper
16	RNAHiSwitch_milestone1_DELETED
17	RNAHiSwitch_paper.tar.gz
18	RNAHiSwitch_paper_DELETED
19	RNAHiSwitch_milestone1
20	RNAHiSwitch_paper
21	Ute_RNASeq_results
22	Ute_miRNA_results_38
23	RNAHiSwitch
24	Data_HepE_Freiburg_PUBLISHED
25	Data_INTENSO_2022-06
26	‘$RECYCLE.BIN’
27	‘System Volume Information’
28	Data_Anna_Mixta_hanseatica_PUBLISHED
29	coi_disclosure.docx
30	Data_Jingang
31	Data_Susanne_16S_re_UNPUBLISHED *
32	Data_Denise_ChIPSeq_Protocol2
33	Data_Caroline_RNAseq_wt_timecourse
34	Data_Caroline_RNAseq_brain_organoids
35	Data_Amir_PUBLISHED_DEL
36	Data_download_virus_fam
37	Data_Gunnar_Yersiniomics_COPYFAILED_DEL
38	Data_Paul_and_Marc_Epidome_batch3
39	ifconfig_hamm.txt
40	Data_Soeren_2023_PUBLISHING
41	Data_Birthe_Svenja_RSV_Probe3_PUBLISHING
42	Data_Ute
43	Data_Susanne_16S_UNPUBLISHED *

/media/jhuang/Seagate Expansion Drive(HOffice)

#	Name
1	SeagateExpansion.ico
2	Autorun.inf
3	Start_Here_Win.exe
4	Warranty.pdf
5	Start_Here_Mac.app
6	Seagate
7	HomeOffice_DIR (Data_Anna_HAPDICS_RNASeq, From_Samsung_T5)
8	DATA_COPY_FROM_178528 (copy_and_clean.sh, logfile_jhuang.log, jhuang)
9	‘System Volume Information’
10	‘$RECYCLE.BIN’

/media/jhuang/Elements(Anna_C.arnes)

#	Name
1	Data_Swantje_HEV_using_viral-ngs
2	VIPER_static_DEL
3	Data_Nicole6_HEV_Swantje1_blood
4	Data_Nicole6_HEV_benchmark
5	Data_Denise_RNASeq_GSE79958
6	Data_16S_Leonie_from_Nico_Gaglianis
7	Fastqs_19-21
8	‘System Volume Information’
9	Data_Luise_Epidome_test
10	Data_Anna_C.acnes_PUBLISHED
11	Data_Denise_LT_DNA_Bindung
12	Data_Denise_LT_K331A_RNASeq
13	Data_Luise_Epidome_batch1
14	Data_Luise_Pseudomonas_aeruginosa_PUBLISHED
15	Data_Luise_Epidome_batch2
16	picrust2_out_2024_2
17	‘$RECYCLE.BIN’

/media/jhuang/Seagate Expansion Drive(DATA_COPY_FROM_hamburg)

#	Name
1	Autorun.inf
2	Start_Here_Win.exe
3	Warranty.pdf
4	Start_Here_Mac.app
5	Seagate
6	DATA_COPY_TRANSFER_INCOMPLETE_DEL
7	DATA_COPY_FROM_hamburg

/media/jhuang/Seagate Expansion Drive(Seagate_1)

#	Name
1	RNA_seq_analysis_tools_2013
2	Data_Laura0
3	Data_Petra_Arck
4	Data_Martin_mycoplasma
5	chromhmm-enhancers
6	ChromHMM_Dir
7	Data_Denise_sT_H3K4me3
8	Data_Denise_sT_H3K27me3
9	Start_Here_Mac.app
10	Seagate
11	Data_Nicole16_parapoxvirus
12	Project_h_rohde_Susanne_WGS_unbiased_DEL.zip
13	Data_Denise_ChIPSeq_Protocol1
14	Data_ENNGS_pathogen_detection_pipeline_comparison
15	j_huang_201904_202002
16	Data_Laura_ChIPseq_GSE120945
17	batch_200314_incomplete
18	m_aepfelbacher.zip
19	m_error_DEL
20	batch_200325
21	batch_200319
22	GAMOLA2_prototyp
23	Data_Nicola_Gagliani
24	2017-18_raw_data
25	Data_Arck_MeDIP
26	trimmed
27	Data_Nicole_16S_Christmas_2020_2
28	j_huang_202007_202012
29	Data_Nicole_16S_Christmas_2020
30	Downloads_2021-01-18_DEL
31	Data_Laura_plasmid
32	Data_Laura_16S_2_re
33	Data_Laura_16S_2
34	Data_Laura_16S_2re
35	Data_Laura_16S_merged
36	Downloads_DEL
37	Data_Laura_16S
38	Data_Anna12_HAPDICS_final
39	‘$RECYCLE.BIN’
40	‘System Volume Information’

/media/jhuang/Seagate Expansion Drive(Seagate_2)

#	Name
1	Data_Nicole4_TH17
2	Start_Here_Win.exe
3	Autorun.inf
4	Warranty.pdf
5	Start_Here_Mac.app
6	Seagate
7	Data_Denise_RNASeq_trimmed_DEL
8	HD12
9	Qi_panGenome
10	ALL
11	fastq_HPI_bw_2019_08_and_2020_02
12	f1_R1_link.sh
13	f1_R2_link.sh
14	rtpd_files
15	m_aepfelbacher.zip
16	Data_Nicole_16S_Hamburg_Odense_Cornell_Muenster
17	HyAsP_incomplete_genomes
18	HyAsP_normal_sampled_input
19	HyAsP_complete_genomes
20	video.zip
21	sam2bedgff.pl
22	HD04.infection.hS_vs_HD04.nose.hS_annotated_degenes.xls
23	ALL83
24	Data_Pietschmann_RSV_Probe_PUBLISHED
25	HyAsP_normal
26	Data_Manthey_16S
27	rtpd_files_DEL
28	HyAsP_bold
29	Data_HEV
30	Seq_VRE_hybridassembly
31	Data_Anna12_HAPDICS_raw_data_shovill_prokka
32	Data_Anna_HAPDICS_WGS_ALL
33	Data_HEV_Freiburg_2020
34	Data_Nicole_HDV_Recombination_PUBLISHED
35	s_hero2x
36	201030_M03701_0207_000000000-J57B4.zip
37	README
38	‘README(1)’
39	dna2.fasta.fai
40	91.pep
41	91.orf
42	91.orf.fai
43	dgaston-dec-06-2012-121211124858-phpapp01.pdf
44	tileshop.fcgi
45	ppat.1009304.s016.tif
46	sequence.txt
47	‘sequence(1).txt’
48	GSE128169_series_matrix.txt.gz
49	GSE128169_family.soft.gz
50	Data_Anna_HAPDICS_RNASeq
51	Data_Christopher_MeDIP_MMc_PUBLISHED
52	Data_Gunnar_Yersiniomics_IMCOMPLETE_DEL
53	Data_Denise_RNASeq
54	‘System Volume Information’
55	‘$RECYCLE.BIN’

/media/jhuang/Elements(An14_RNAs)

#	Name
1	Data_Anna10_RP62A
2	Data_Nicole12_16S_Kluwe_Bunders
3	chromhmm-enhancers
4	Data_Denise_sT_Methylation
5	Data_Denise_LTtrunc_Methylation
6	Data_16S_arckNov
7	Data_Tabea_RNASeq
8	nr_gz_README
9	j_huang_raw_fq
10	‘System Volume Information’
11	‘$RECYCLE.BIN’
12	host_refs
13	Vraw
14	Data_Susanne_Amplicon_RdRp_orf1_2 *
15	tmp
16	Data_RNA188_Paul_Becher
17	Data_ChIPSeq_Laura
18	Data_16S_arckNov_review_PUBLISHED
19	Data_16S_arckNov_re
20	Fastqs
21	Data_Tabea_RNASeq_submission
22	Data_Anna_Cutibacterium_acnes_DEL
23	Data_Silvia_RNASeq_SUBMISSION
24	Data_Hannes_ChIPSeq
25	Data_Anna14_RNASeq_to_be_DEL
26	Data_Pietschmann_RSV_Probe2_PUBLISHED
27	Data_Holger_Klebsiella_pneumoniae_SNP_PUBLISHING
28	Data_Anna14_RNASeq_plus_public

/media/jhuang/Elements(Indra_HAPDICS)

#	Name
1	Data_Anna11_Sepdermidis_DEL
2	HD15_without_10
3	HD31
4	HD33
5	HD39
6	HD43
7	HD46
8	HD15_with_10
9	HD26
10	HD59
11	HD25
12	HD21
13	HD17
14	HD04
15	Data_Anna11_Pair1-6_P6
16	Data_Anna12_HAPDICS_HyAsP
17	HAPDICS_hyasp_plasmids
18	Data_Anna_HAPDICS_review
19	data_overview.txt
20	align_assem_res_DEL
21	‘System Volume Information’
22	EXCHANGE_DEL
23	Data_Indra_H3K4me3_public
24	Data_Gunnar_MS
25	‘$RECYCLE.BIN’
26	UKE_DELLWorkstation_C_Users_indbe_Desktop
27	Linux_DELLWorkstation_C_Users_indbe_VirtualBoxVMs
28	Data_Anna_HAPDICS_RNASeq_rawdata
29	Data_Indra_H3K27ac_public
30	Data_Holger_Klebsiella_pneumoniae_SNP_PUBLISHING
31	DATA_INDRA_RNASEQ
32	DATA_INDRA_CHIPSEQ

/media/jhuang/Elements(jhuang_*)

#	Name
1	‘Install Western Digital Software for Windows.exe’
2	‘Install Western Digital Software for Mac.dmg’
3	‘System Volume Information’
4	‘$RECYCLE.BIN’
5	20250203_FS10003086_95_BTR67811-0621

/media/jhuang/Smarty

#	Name
1	lost+found
2	Blast_db
3	temporary_files_DEL
4	ALIGN_ASSEM
5	Data_Paul_Staphylococcus_epidermidis
6	Data_16S_Degenhardt_Marius_DEL
7	Data_Gunnar_Yersiniomics_DEL
8	Data_Manja_RNAseq_Organoids_Virus
9	Data_Emilia_MeDIP
10	DjangoApp_Backup_2023-10-30
11	ref
12	Data_Michelle_RNAseq_2025_raw_data_DEL_AFTER_UPLOAD_GEO

Original input (as one point)

/media/jhuang/INTENSO is empty --> Now the data are on ~/DATA_Intenso
/dev/sdg1       3,7T  512K  3,7T   1% /media/jhuang/INTENSO

jhuang@WS-2290C:~/DATA$ ls -tlrh
total 1,6M
drwxrwxrwx   6 jhuang jhuang 4,0K Okt 26  2022 Data_Ute_MKL1
drwxrwxrwx   8 jhuang jhuang 4,0K Jan 13  2023 Data_Ute_RNA_4_2022-11_test
drwxrwxr-x   7 jhuang jhuang 4,0K Mär  8  2023 Data_Ute_RNA_3
drwxr-xr-x  11 jhuang jhuang 4,0K Dez 19  2023 Data_Susanne_Carotis_RNASeq_PUBLISHING
drwxr-xr-x  21 jhuang jhuang 4,0K Jun 18  2024 Data_Jiline_Yersinia_SNP
drwxrwxr-x   5 jhuang jhuang 4,0K Jul 22  2024 Data_Tam_ABAYE_RS05070_on_A_calcoaceticus_baumannii_complex_DUPLICATED_DEL
drwxr-xr-x   2 jhuang jhuang 4,0K Jul 23  2024 Data_Nicole_CRC1648
drwxr-xr-x   4 jhuang jhuang 4,0K Sep  6  2024 Mouse_HS3ST1_12373_out
drwxr-xr-x   4 jhuang jhuang 4,0K Sep  6  2024 Mouse_HS3ST1_12175_out
drwxrwxr-x  10 jhuang jhuang 4,0K Sep 12  2024 Data_Biobakery
drwxrwxr-x   6 jhuang jhuang 4,0K Sep 23  2024 Data_Xiaobo_10x_2
drwxr-xr-x   4 jhuang jhuang 4,0K Sep 23  2024 Data_Xiaobo_10x_3
drwxr-xr-x   3 jhuang jhuang 4,0K Sep 26  2024 Talk_Nicole_CRC1648
drwxr-xr-x   2 jhuang jhuang 4,0K Sep 26  2024 Talks_Bioinformatics_Meeting
drwxr-xr-x   2 jhuang jhuang  12K Sep 26  2024 Talks_resources
drwxrwxr-x   6 jhuang jhuang  12K Okt 10  2024 Data_Susanne_MPox_DAMIAN
drwxrwxr-x   3 jhuang jhuang 4,0K Okt 14  2024 Data_host_transcriptional_response
drwxr-xr-x  13 jhuang jhuang 4,0K Okt 23  2024 Talks_including_DEEP-DV
drwxrwxr-x   2 jhuang jhuang 4,0K Okt 24  2024 DOKTORARBEIT
drwxrwxr-x  18 jhuang jhuang 4,0K Nov 11  2024 Data_Susanne_MPox
drwxrwxr-x  25 jhuang jhuang  12K Nov 11  2024 Data_Jiline_Transposon
drwxrwxr-x  16 jhuang jhuang  20K Nov 25  2024 Data_Jiline_Transposon2
drwxrwxr-x   3 jhuang jhuang 4,0K Dez 13  2024 Data_Matlab
drwxrwxr-x   5 jhuang jhuang 4,0K Jan 28  2025 deepseek-ai
drwx------   4 jhuang jhuang 4,0K Feb  5  2025 Stick_Mi_DEL
-rw-rw-r--   1 jhuang jhuang 1,1K Feb 18  2025 TODO_shares
drwxrwxrwx  13 jhuang jhuang 4,0K Mär  3  2025 Data_Ute_RNA_4
drwxrwxr-x   2 jhuang jhuang 4,0K Mär 31  2025 Data_Liu_PCA_plot
-rw-rw-r--   1 jhuang jhuang  43K Apr  3  2025 README_run_viral-ngs_inside_Docker
-rw-rw-r--   1 jhuang jhuang 8,7K Apr  9  2025 README_compare_genomes
-rw-rw-r--   1 jhuang jhuang    0 Apr 11  2025 mapped.bam
drwxrwxr-x   3 jhuang jhuang 4,0K Apr 24  2025 Data_Serpapi
drwxrwxrwx  22 jhuang jhuang 4,0K Apr 30  2025 Data_Ute_RNA_1_2
drwxrwxr-x  15 jhuang jhuang 4,0K Apr 30  2025 Data_Marc_RNAseq_2024
drwxrwxr-x  45 jhuang jhuang  12K Mai 15  2025 Data_Nicole_CaptureProbeSequencing
-rw-rw-r--   1 jhuang jhuang  657 Mai 23  2025 LOG_mapping
drwxrwxr-x  46 jhuang jhuang 4,0K Mai 26  2025 Data_Huang_Human_herpesvirus_3
drwxrwxr-x   8 jhuang jhuang 4,0K Jun 13  2025 Data_Nicole_DAMIAN_Post-processing_Pathoprobe_FluB_Links
lrwxrwxrwx   1 jhuang jhuang   37 Jun 16  2025 Access_to_Win7 -> ./Data_Marius_16S/picrust2_out_2024_2
drwxrwxr-x  17 jhuang jhuang 4,0K Jun 18  2025 Data_DAMIAN_Post-processing_Flavivirus_and_FSME_and_Haemophilus
drwxr-xr-x  42 jhuang jhuang  36K Jun 23  2025 Data_Luise_Sepi_STKN
drwxrwxr-x  29 jhuang jhuang  20K Jul 22  2025 Data_Patricia_Sepi_7samples
drwxr-xr-x   9 jhuang jhuang 4,0K Aug  8  2025 Data_Soeren_2025_PUBLISHING
drwxrwxr-x   9 jhuang jhuang 4,0K Aug 13  2025 Data_Ben_RNAseq_2025
drwxrwxr-x  34 jhuang jhuang  12K Sep  3 12:18 Data_Tam_DNAseq_2025_AYE-WT_Q_S_craA-Tig4_craA-1-Cm200_craA-2-Cm200
drwxrwxr-x  50 jhuang jhuang  16K Okt  6 17:59 Data_Patricia_Transposon
drwxrwxr-x  23 jhuang jhuang  12K Okt 20 13:27 Data_Patricia_Transposon_2025
drwxrwxr-x   2 jhuang jhuang 4,0K Okt 23 12:21 Colocation_Space
drwxrwxr-x   2 jhuang jhuang 4,0K Okt 27 12:56 Data_Tam_Methylation_2025_empty
-rw-rw-r--   1 jhuang jhuang 151K Nov  3 13:01 2025-11-03_eVB-Schreiben_12-57.pdf
-rw-rw-r--   1 jhuang jhuang  67K Nov  5 16:59 DEGs_Group1_A1-A3+A8-A10_vs_Group2_B10-B16.png
-rw-rw-r--   1 jhuang jhuang 687K Nov 14 09:55 README.pdf
drwxrwxr-x   2 jhuang jhuang 4,0K Nov 24 15:43 Data_Hannes_JCM00612
drwxrwxr-x   3 jhuang jhuang 4,0K Dez  4 17:03 167_redundant_DEL
drwxrwxr-x   2 jhuang jhuang 4,0K Dez  8 10:33 Lehre_Bioinformatik
drwxrwxr-x  27 jhuang jhuang  12K Dez  8 11:29 Data_Ben_Boruta_Analysis
drwxrwxr-x  18 jhuang jhuang 4,0K Dez  8 17:39 Data_Childrensclinic_16S_2025_DEL
drwxrwxr-x   2 jhuang jhuang 4,0K Dez 10 10:05 Data_Ben_Mycobacterium_pseudoscrofulaceum
-rw-rw-r--   1 jhuang jhuang 8,9K Dez 15 12:42 Foong_RNA_mSystems_Huang_Changed.txt
drwxrwxr-x  22 jhuang jhuang 4,0K Dez 17 13:07 Data_Pietro_Scatturo_and_Charlotte_Uetrecht_16S_2025
drwxrwxr-x   8 jhuang jhuang 4,0K Dez 18 10:45 Data_JuliaBerger_RNASeq_SARS-CoV-2
drwxrwxr-x  19 jhuang jhuang 4,0K Jan  3 17:42 Data_PaulBongarts_S.epidermidis_HDRNA
lrwxrwxrwx   1 jhuang jhuang   31 Jan 12 14:30 Data_Ute -> /media/jhuang/Elements/Data_Ute
drwxrwxr-x  12 jhuang jhuang 4,0K Jan 16 12:44 Data_Foong_DNAseq_2025_AYE_Dark_vs_Light_TODO
drwxrwxrwx  22 jhuang jhuang 4,0K Jan 16 12:48 Data_Foong_RNAseq_2021_ATCC19606_Cm
drwxrwxr-x   2 jhuang jhuang 4,0K Jan 16 13:02 Data_Tam_Funding
drwxrwxr-x   9 jhuang jhuang 4,0K Jan 16 13:32 Data_Tam_RNAseq_2025_LB-AB_IJ_W1_Y1_WT_vs_Mac-AB_IJ_W1_Y1_WT_on_ATCC19606
drwxrwxr-x  12 jhuang jhuang 4,0K Jan 16 13:32 Data_Tam_RNAseq_2025_subMIC_exposure_on_ATCC19606
-rw-rw-r--   1 jhuang jhuang 1,2K Jan 16 13:34 Data_Tam.txt
drwxrwxr-x  16 jhuang jhuang 4,0K Jan 16 13:37 Data_Tam_RNAseq_2024_AUM_MHB_Urine_on_ATCC19606
drwxrwxr-x  10 jhuang jhuang 4,0K Jan 16 18:22 Data_Tam_Metagenomics_2026
drwxrwxr-x   6 jhuang jhuang  16K Jan 23 16:35 Data_Michelle
drwxrwxr-x  38 jhuang jhuang  12K Jan 28 15:20 Data_Nicole_16S_2025_Childrensclinic
drwxr-xr-x 145 jhuang jhuang  36K Jan 29 10:49 Data_Sophie_HDV_Sequences
drwxrwxr-x   4 jhuang jhuang 4,0K Jan 30 11:44 Data_Tam_DNAseq_2026_19606deltaIJfluE
-rw-rw-r--   1 jhuang jhuang  63K Jan 30 17:53 README_nf-core
drwxrwxr-x  22 jhuang jhuang 4,0K Feb  4 10:43 Data_Vero_Kymographs
drwxrwxr-x  13 jhuang jhuang 4,0K Feb  4 14:06 Access_to_Win10
drwxrwxr-x   7 jhuang jhuang 4,0K Feb  5 11:59 Data_Patricia_AMRFinderPlus_2025
drwxrwxr-x  45 jhuang jhuang 4,0K Feb  6 11:54 Data_Tam_DNAseq_2025_Unknown-adeABadeIJ_adeIJK_CM1_CM2
drwxrwxr-x  41 jhuang jhuang  12K Feb  9 15:11 Data_Damian
drwxrwxr-x   6 jhuang jhuang 4,0K Feb 13 12:48 Data_Karoline_16S
drwxrwxr-x  13 jhuang jhuang  12K Feb 13 18:09 Data_JuliaFuchs_RNAseq_2025
drwxrwxr-x  18 jhuang jhuang 4,0K Feb 16 11:19 Data_Tam_DNAseq_2025_ATCC19606-Y1Y2Y3Y4W1W2W3W4_TODO
drwxrwxr-x  34 jhuang jhuang 4,0K Feb 16 15:54 Data_Tam_DNAseq_2026_Acinetobacter_harbinensis
drwxrwxr-x  19 jhuang jhuang 4,0K Feb 16 17:13 Data_Benjamin_DNAseq_2026_GE11174
drwxrwxrwx  36 jhuang jhuang  12K Feb 17 15:02 Data_Susanne_spatialRNA_2022.9.1_backup
drwxrwxr-x  39 jhuang jhuang  12K Feb 17 15:12 Data_Susanne_spatialRNA

jhuang@WS-2290C:~/DATA_A$ ls -ltrh
total 24K
drwxr-xr-x  7 jhuang jhuang 4,0K Jun 18  2024 Data_Damian_NEW_CREATED
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024 Data_R_bubbleplots
drwxr-xr-x 16 jhuang jhuang 4,0K Jun 18  2024 Data_Ute_TRANSFERED_DEL
drwxr-xr-x  2 jhuang jhuang 4,0K Okt  7  2024 Paper_Target_capture_sequencing_MHH_PUBLISHED
drwxr-xr-x 20 jhuang jhuang 4,0K Okt  8  2024 Data_Nicole8_Lamprecht_new_PUBLISHED
drwxrwxrwx  8 jhuang jhuang 4,0K Mai 21  2025 Data_Samira_RNAseq

jhuang@WS-2290C:~/DATA_B$ ls -tlrh
total 136K
drwxr-xr-x  3 jhuang jhuang 4,0K Jun 18  2024 Data_DAMIAN_endocarditis_encephalitis
drwxr-xr-x  8 jhuang jhuang 4,0K Jun 18  2024 Data_Denise_sT_PUBLISHING
drwxr-xr-x 12 jhuang jhuang 4,0K Jun 18  2024 Data_Fran2_16S_func
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024 Data_Holger_5179-R1_vs_5179
drwxr-xr-x 16 jhuang jhuang 4,0K Jun 18  2024 Antraege_
drwxr-xr-x 18 jhuang jhuang 4,0K Jun 18  2024 Data_16S_Nicole_210222
drwxr-xr-x  6 jhuang jhuang 4,0K Jun 18  2024 Data_Adam_Influenza_A_virus
drwxr-xr-x 14 jhuang jhuang  12K Jun 18  2024 Data_Anna_Efaecium_assembly
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024 Data_Bactopia
drwxr-xr-x  5 jhuang jhuang 4,0K Jun 18  2024 Data_Ben_RNAseq
drwxr-xr-x  7 jhuang jhuang 4,0K Jun 18  2024 Data_Johannes_PIV3
drwxr-xr-x 19 jhuang jhuang 4,0K Jun 18  2024 Data_Luise_Epidome_longitudinal_nose
drwxr-xr-x  6 jhuang jhuang 4,0K Jun 18  2024 Data_Manja_Hannes_Probedesign
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024 Data_Marc_AD_PUBLISHING
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024 Data_Marc_RNA-seq_Saureus_Review
drwxr-xr-x 17 jhuang jhuang 4,0K Jun 18  2024 Data_Nicole_16S
drwxr-xr-x  3 jhuang jhuang 4,0K Jun 18  2024 Data_Nicole_cfDNA_pathogens
drwxr-xr-x 16 jhuang jhuang 4,0K Jun 18  2024 Data_Ring_and_CSF_PegivirusC_DAMIAN
drwxr-xr-x  4 jhuang jhuang 4,0K Jun 18  2024 Data_Song_Microarray
drwxr-xr-x 11 jhuang jhuang 4,0K Jun 18  2024 Data_Susanne_Omnikron
drwxr-xr-x  3 jhuang jhuang 4,0K Jun 18  2024 Data_Viro
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024 Doktorarbeit
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024 Poster_Rohde_20230724
drwxr-xr-x  6 jhuang jhuang 4,0K Jul 12  2024 Data_Django
drwxr-xr-x 35 jhuang jhuang 4,0K Okt 21  2024 Data_Holger_S.epidermidis_1585_5179_HD05
drwxr-xr-x  9 jhuang jhuang 4,0K Nov 18  2024 Data_Manja_RNAseq_Organoids_Virus
drwxr-xr-x  2 jhuang jhuang 4,0K Feb 21  2025 Data_Holger_MT880870_MT880872_Annotation
drwxr-xr-x 12 jhuang jhuang 4,0K Apr  8  2025 Data_Soeren_RNA-seq_2022
drwxr-xr-x  5 jhuang jhuang 4,0K Apr 11  2025 Data_Manja_RNAseq_Organoids_Merged
drwxr-xr-x 24 jhuang jhuang 4,0K Apr 25  2025 Data_Gunnar_Yersiniomics
drwxr-xr-x 10 jhuang jhuang 4,0K Jan 16 17:14 Data_Manja_RNAseq_Organoids
drwxr-xr-x  3 jhuang jhuang 4,0K Feb 17 12:11 Data_Susanne_Carotis_MS

jhuang@WS-2290C:~/DATA_C$ ls -tlrh
total 13G
-rwxr-xr-x  1 jhuang jhuang 1,7M Jun 18  2024  2022-10-27_IRI_manuscript_v03_JH.docx
-rwxr-xr-x  1 jhuang jhuang 7,1K Jun 18  2024  16304905.fasta
-rwxr-xr-x  1 jhuang jhuang  55K Jun 18  2024 '16S data manuscript_NF.docx'
-rwxr-xr-x  1 jhuang jhuang 792K Jun 18  2024  180820_2_supp_4265595_sw6zjk.docx
-rwxr-xr-x  1 jhuang jhuang  17K Jun 18  2024  180820_2_supp_4265596_sw6zjk.docx
-rwxr-xr-x  1 jhuang jhuang  12K Jun 18  2024  1a_vs_3.csv
-rwxr-xr-x  1 jhuang jhuang  90K Jun 18  2024 '2.05.01.05-A01 Urlaubsantrag-Shuting-beantragt.pdf'
-rwxr-xr-x  1 jhuang jhuang 708K Jun 18  2024  2014SawickaBBA.pdf
-rwxr-xr-x  1 jhuang jhuang  61K Jun 18  2024  20160509Manuscript_NDM_OXA_mitKomm.doc
-rwxr-xr-x  1 jhuang jhuang 289K Jun 18  2024  220607_Agenda_monthly_meeting.pdf
-rwxr-xr-x  1 jhuang jhuang  14K Jun 18  2024 '20221129 Table mutations.docx'
-rwxr-xr-x  1 jhuang jhuang  12G Jun 18  2024  230602_NB501882_0428_AHKG53BGXT.zip
-rwxr-xr-x  1 jhuang jhuang 107K Jun 18  2024  362383173.rar
-rwxr-xr-x  1 jhuang jhuang 128K Jun 18  2024  562.9459.1.fa
-rwxr-xr-x  1 jhuang jhuang 126K Jun 18  2024  562.9459.1_rc.fa
-rwxr-xr-x  1 jhuang jhuang 1,6M Jun 18  2024  ASA3P.pdf
-rwxr-xr-x  1 jhuang jhuang  21K Jun 18  2024  All_indels_annotated_vHR.xlsx
-rwxr-xr-x  1 jhuang jhuang  11K Jun 18  2024 'Amplikon_indeces_Susanne +groups.xlsx'
-rwxr-xr-x  1 jhuang jhuang 9,6K Jun 18  2024  Amplikon_indeces_Susanne.xlsx
-rwxr-xr-x  1 jhuang jhuang   68 Jun 18  2024  GAMOLA2
-rwxr-xr-x  1 jhuang jhuang   88 Jun 18  2024  Data_Susanne_Carotis_spatialRNA_PUBLISHING
-rwxr-xr-x  1 jhuang jhuang  112 Jun 18  2024  Data_Paul_Staphylococcus_epidermidis
-rwxr-xr-x  1 jhuang jhuang  118 Jun 18  2024  Data_Nicola_Schaltenberg_PICRUSt
-rwxr-xr-x  1 jhuang jhuang  100 Jun 18  2024  Data_Nicola_Schaltenberg
-rwxr-xr-x  1 jhuang jhuang   94 Jun 18  2024  Data_Nicola_Gagliani
-rwxr-xr-x  1 jhuang jhuang   96 Jun 18  2024  Data_methylome_MMc
-rwxr-xr-x  1 jhuang jhuang   78 Jun 18  2024  Data_Jingang
-rwxr-xr-x  1 jhuang jhuang  112 Jun 18  2024  Data_Indra_RNASeq_GSM2262901
-rwxr-xr-x  1 jhuang jhuang   84 Jun 18  2024  Data_Holger_VRE
-rwxr-xr-x  1 jhuang jhuang  128 Jun 18  2024  Data_Holger_Pseudomonas_aeruginosa_SNP
-rwxr-xr-x  1 jhuang jhuang   92 Jun 18  2024  Data_Hannes_ChIPSeq
-rwxr-xr-x  1 jhuang jhuang   76 Jun 18  2024  Data_Emilia_MeDIP
-rwxr-xr-x  1 jhuang jhuang   88 Jun 18  2024  Data_ChristophFR_HepE_published
-rwxr-xr-x  1 jhuang jhuang  158 Jun 18  2024  Data_Christopher_MeDIP_MMc_published
-rwxr-xr-x  1 jhuang jhuang  104 Jun 18  2024  Data_Anna_Kieler_Sepi_Staemme
-rwxr-xr-x  1 jhuang jhuang  136 Jun 18  2024  Data_Anna12_HAPDICS_final
-rwxr-xr-x  1 jhuang jhuang   96 Jun 18  2024  Data_Anastasia_RNASeq_PUBLISHING
-rwxr-xr-x  1 jhuang jhuang 169K Jun 18  2024  Aufnahmeantrag_komplett_10_2022.pdf
-rwxr-xr-x  1 jhuang jhuang 1,2M Jun 18  2024  Astrovirus.pdf
-rwxr-xr-x  1 jhuang jhuang  732 Jun 18  2024  COMMANDS
-rwxr-xr-x  1 jhuang jhuang  690 Jun 18  2024  Bacterial_pipelines.txt
-rwxr-xr-x  1 jhuang jhuang  16M Jun 18  2024  COMPSRA_uke_DEL.jar
-rwxr-xr-x  1 jhuang jhuang 239K Jun 18  2024  ChIPSeq_pipeline_desc.docx
-rwxr-xr-x  1 jhuang jhuang 385K Jun 18  2024  ChIPSeq_pipeline_desc.pdf
-rwxr-xr-x  1 jhuang jhuang 2,1M Jun 18  2024  Comparative_genomic_analysis_of_eight_novel_haloal.pdf
-rwxr-xr-x  1 jhuang jhuang  64K Jun 18  2024  CvO_Klassenliste_7_3.pdf
-rwxr-xr-x  1 jhuang jhuang 649K Jun 18  2024 'Copy of pool_b1_CGATGT_300.xlsx'
-rwxr-xr-x  1 jhuang jhuang 3,9K Jun 18  2024  Fran_16S_Exp8-17-21-27.txt
-rwxr-xr-x  1 jhuang jhuang  463 Jun 18  2024  HPI_DRIVE
-rwxr-xr-x  1 jhuang jhuang 179K Jun 18  2024  HEV_aligned.fasta
-rwxr-xr-x  1 jhuang jhuang 4,1K Jun 18  2024  INTENSO_DIR
-rwxr-xr-x  1 jhuang jhuang  14K Jun 18  2024  HPI_samples_for_NGS_29.09.22.xlsx
-rwxr-xr-x  1 jhuang jhuang 4,3K Jun 18  2024  Hotmail_to_Gmail
-rwxr-xr-x  1 jhuang jhuang  13M Jun 18  2024  Indra_Thesis_161020.pdf
-rwxr-xr-x  1 jhuang jhuang 5,2K Jun 18  2024 'LT K331A.gbk'
-rwxr-xr-x  1 jhuang jhuang    0 Jun 18  2024  LOG_p954_stat
-rwxr-xr-x  1 jhuang jhuang 684K Jun 18  2024  LOG
-rwxr-xr-x  1 jhuang jhuang 197K Jun 18  2024  Manuscript_10_02_2021.docx
-rwxr-xr-x  1 jhuang jhuang 595K Jun 18  2024  Metagenomics_Tools_and_Insights.pdf
-rwxr-xr-x  1 jhuang jhuang  14K Jun 18  2024 'Miseq Amplikon LAuf April.xlsx'
-rwxr-xr-x  1 jhuang jhuang 2,2M Jun 18  2024  NGS.tar.gz
-rwxr-xr-x  1 jhuang jhuang 586K Jun 18  2024  Nachweis_Bakterien_Viren_im_Hochdurchsatz.pdf
-rwxr-xr-x  1 jhuang jhuang 1,2K Jun 18  2024  Nicole8_Lamprecht_logs
-rwxr-xr-x  1 jhuang jhuang  24M Jun 18  2024  Nanopore.handouts.pdf
-rwxr-xr-x  1 jhuang jhuang 113K Jun 18  2024 'Norovirus paper Susanne 191105.docx'
-rwxr-xr-x  1 jhuang jhuang 503K Jun 18  2024  PhyloRNAalifold.pdf
-rwxr-xr-x  1 jhuang jhuang  19K Jun 18  2024  README_R
-rwxr-xr-x  1 jhuang jhuang 137K Jun 18  2024  README_RNAHiSwitch_DEL
-rwxr-xr-x  1 jhuang jhuang 8,3M Jun 18  2024  RNA-NGS_Analysis_modul3_NanoStringNorm.zip
-rwxr-xr-x  1 jhuang jhuang  57K Jun 18  2024  RNAConSLOptV1.2.tar.gz
-rwxr-xr-x  1 jhuang jhuang  17K Jun 18  2024 'RSV GFP5 including 3`UTR.docx'
-rwxr-xr-x  1 jhuang jhuang  238 Jun 18  2024  SNPs_on_pangenome.txt
-rwxr-xr-x  1 jhuang jhuang   55 Jun 18  2024  SERVER
-rwxr-xr-x  1 jhuang jhuang  26M Jun 18  2024  R_tutorials-master.zip
-rwxr-xr-x  1 jhuang jhuang 182K Jun 18  2024  Rawdata_Readme.pdf
-rwxr-xr-x  1 jhuang jhuang  40K Jun 18  2024  SUB10826945_record_preview.txt
-rwxr-xr-x  1 jhuang jhuang 283K Jun 18  2024  S_staphylococcus_annotated_diff_expr.xls
-rwxr-xr-x  1 jhuang jhuang 2,0K Jun 18  2024  Snakefile_list
-rwxr-xr-x  1 jhuang jhuang 160K Jun 18  2024  Source_Classification_Code.rds
-rwxr-xr-x  1 jhuang jhuang  61K Jun 18  2024  Supplementary_Table_S3.xlsx
-rwxr-xr-x  1 jhuang jhuang  617 Jun 18  2024  Untitled.ipynb
-rwxr-xr-x  1 jhuang jhuang 127M Jun 18  2024  UniproUGENE_UserManual.pdf
-rwxr-xr-x  1 jhuang jhuang  14M Jun 18  2024  Untitled1.ipynb
-rwxr-xr-x  1 jhuang jhuang 110K Jun 18  2024  Untitled2.ipynb
-rwxr-xr-x  1 jhuang jhuang 2,9K Jun 18  2024  Untitled3.ipynb
-rwxr-xr-x  1 jhuang jhuang  18K Jun 18  2024  WAC6h_vs_WAP6h_down.txt
-rwxr-xr-x  1 jhuang jhuang  100 Jun 18  2024  damian_nodbs
-rwxr-xr-x  1 jhuang jhuang  45K Jun 18  2024  WAC6h_vs_WAP6h_up.txt
-rwxr-xr-x  1 jhuang jhuang 635K Jun 18  2024 'add. Figures Hamburg_UKE.pptx'
-rwxr-xr-x  1 jhuang jhuang 3,7M Jun 18  2024  all_gene_counts_with_annotation.xlsx
-rwxr-xr-x  1 jhuang jhuang  22K Jun 18  2024  app_flask.py
-rwxr-xr-x  1 jhuang jhuang 1,8K Jun 18  2024  bengal-bay-0.1.json
-rwxr-xr-x  1 jhuang jhuang  16K Jun 18  2024  bengal3_ac3.yml
-rwxr-xr-x  1 jhuang jhuang 246K Jun 18  2024  call_shell_from_Ruby.png
-rwxr-xr-x  1 jhuang jhuang 8,1K Jun 18  2024  bengal3_ac3_.yml
-rwxr-xr-x  1 jhuang jhuang   12 Jun 18  2024  empty.fasta
-rwxr-xr-x  1 jhuang jhuang  32K Jun 18  2024  coefficients_csaw_vs_diffreps.xlsx
-rwxr-xr-x  1 jhuang jhuang 4,3K Jun 18  2024  exchange.txt
-rwxr-xr-x  1 jhuang jhuang  30M Jun 18  2024  exdata-data-NEI_data.zip
-rwxr-xr-x  1 jhuang jhuang 6,6K Jun 18  2024  genes_wac6_wap6.xls
-rwxr-xr-x  1 jhuang jhuang 115M Jun 18  2024  go1.13.linux-amd64.tar.gz.1
-rwxr-xr-x  1 jhuang jhuang  29K Jun 18  2024  hev_p2-p5.fa
-rwxr-xr-x  1 jhuang jhuang 3,8K Jun 18  2024  map_corrected_backup.txt
-rwxr-xr-x  1 jhuang jhuang  325 Jun 18  2024  install_nginx_on_hamm
-rwxr-xr-x  1 jhuang jhuang  20M Jun 18  2024  hg19.rmsk.bed
-rwxr-xr-x  1 jhuang jhuang 107K Jun 18  2024  metadata-9563675-processed-ok.tsv
-rwxr-xr-x  1 jhuang jhuang 288K Jun 18  2024  mkg_sprechstundenflyer_ver1b_dezember_2019.pdf
-rwxr-xr-x  1 jhuang jhuang  588 Jun 18  2024  multiqc_config.yaml
-rwxr-xr-x  1 jhuang jhuang  38K Jun 18  2024  p11326_OMIKRON3398_corsurv.gb
-rwxr-xr-x  1 jhuang jhuang  30K Jun 18  2024  p11326_OMIKRON3398_corsurv.gb_converted.fna
-rwxr-xr-x  1 jhuang jhuang 3,9K Jun 18  2024  parseGenbank_reformat.py
-rwxr-xr-x  1 jhuang jhuang 222K Jun 18  2024  pangenome-snakemake-master.zip
-rwxr-xr-x  1 jhuang jhuang 283K Jun 18  2024 'phylo tree draft.pdf'
-rwxr-xr-x  1 jhuang jhuang  125 Jun 18  2024  qiime_params.txt
-rwxr-xr-x  1 jhuang jhuang 2,3M Jun 18  2024  pool_b1_CGATGT_300.zip
-rwxr-xr-x  1 jhuang jhuang 5,5K Jun 18  2024  qiime_params_backup.txt
-rwxr-xr-x  1 jhuang jhuang 4,5K Jun 18  2024  qiime_params_s16_s18.txt
-rwxr-xr-x  1 jhuang jhuang   68 Jun 18  2024  snakePipes
-rwxr-xr-x  1 jhuang jhuang  25K Jun 18  2024  results_description.html
-rwxr-xr-x  1 jhuang jhuang 139M Jun 18  2024  rnaalihishapes.tar.gz
-rwxr-xr-x  1 jhuang jhuang 3,4M Jun 18  2024  rnaseq_length_bias.pdf
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  3932-Leber
drwxr-xr-x  6 jhuang jhuang 4,0K Jun 18  2024  BioPython
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  Biopython
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  DEEP-DV
drwxr-xr-x 13 jhuang jhuang 4,0K Jun 18  2024  DOKTORARBEIT
drwxr-xr-x 17 jhuang jhuang 4,0K Jun 18  2024  Data_16S_Arck_vaginal_stool
drwxr-xr-x 22 jhuang jhuang 4,0K Jun 18  2024  Data_16S_BS052
drwxr-xr-x 13 jhuang jhuang 4,0K Jun 18  2024  Data_16S_Birgit
drwxr-xr-x  3 jhuang jhuang 4,0K Jun 18  2024  Data_16S_Christner
drwxr-xr-x  9 jhuang jhuang 4,0K Jun 18  2024  Data_16S_Leonie
drwxr-xr-x 11 jhuang jhuang 4,0K Jun 18  2024  Data_16S_PatientA-G_CSF
drwxr-xr-x 14 jhuang jhuang 4,0K Jun 18  2024  Data_16S_Schaltenberg
drwxr-xr-x  7 jhuang jhuang 4,0K Jun 18  2024  Data_16S_benchmark
drwxr-xr-x  7 jhuang jhuang 4,0K Jun 18  2024  Data_16S_benchmark2
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  Data_16S_gcdh_BKV
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  Data_Alex1_Amplicon
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  Data_Alex1_SNP
drwxr-xr-x  5 jhuang jhuang 4,0K Jun 18  2024  Data_Analysis_for_Life_Science
drwxr-xr-x 19 jhuang jhuang 4,0K Jun 18  2024  Data_Anna13_vanA-Element
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  Data_Anna14_PACBIO_methylation
drwxr-xr-x  8 jhuang jhuang 4,0K Jun 18  2024  Data_Anna_C.acnes2_old_DEL
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  Data_Anna_MT880872_update
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  Data_Anna_gap_filling_agrC
drwxr-xr-x  4 jhuang jhuang 4,0K Jun 18  2024  Data_Baechlein_Hepacivirus_2018
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  Data_Bornavirus
drwxr-xr-x  3 jhuang jhuang 4,0K Jun 18  2024  Data_CSF
drwxr-xr-x  9 jhuang jhuang 4,0K Jun 18  2024  Data_Christine_cz19-178-rothirsch-bovines-hepacivirus
drwxr-xr-x  4 jhuang jhuang 4,0K Jun 18  2024  Data_Daniela_adenovirus_WGS
drwxr-xr-x  3 jhuang jhuang 4,0K Jun 18  2024  Data_Emilia_MeDIP_DEL
drwxr-xr-x 14 jhuang jhuang 4,0K Jun 18  2024  Data_Francesco2021_16S
drwxr-xr-x  9 jhuang jhuang 4,0K Jun 18  2024  Data_Francesco2021_16S_re
drwxr-xr-x  3 jhuang jhuang 4,0K Jun 18  2024  Data_Gunnar_MS
drwxr-xr-x 10 jhuang jhuang 4,0K Jun 18  2024  Data_Hannes_RNASeq
drwxr-xr-x 29 jhuang jhuang 4,0K Jun 18  2024  Data_Holger_Efaecium_variants_PUBLISHED
drwxr-xr-x  5 jhuang jhuang 4,0K Jun 18  2024  Data_Holger_VRE_DEL
drwxr-xr-x  3 jhuang jhuang 4,0K Jun 18  2024  Data_Icebear_Damian
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  Data_Indra3_H3K4_p2_DEL
drwxr-xr-x  4 jhuang jhuang 4,0K Jun 18  2024  Data_Indra6_RNASeq_ChipSeq_Integration_DEL
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  Data_Indra_Figures
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  Data_KatjaGiersch_new_HDV
drwxr-xr-x  3 jhuang jhuang 4,0K Jun 18  2024  Data_MHH_Encephalitits_DAMIAN
drwxr-xr-x  6 jhuang jhuang 4,0K Jun 18  2024  Data_Manja_RPAChIPSeq_public
drwxr-xr-x 72 jhuang jhuang  12K Jun 18  2024  Data_Manuel_WGS_Yersinia
drwxr-xr-x 32 jhuang jhuang 4,0K Jun 18  2024  Data_Manuel_WGS_Yersinia2_DEL
drwxr-xr-x  4 jhuang jhuang 4,0K Jun 18  2024  Data_Manuel_WGS_Yersinia_DEL
drwxr-xr-x 13 jhuang jhuang 4,0K Jun 18  2024  Data_Marcus_tracrRNA_structures
drwxr-xr-x  5 jhuang jhuang 4,0K Jun 18  2024  Data_Mausmaki_Damian
drwxr-xr-x  4 jhuang jhuang 4,0K Jun 18  2024  Data_Nicole1_Tropheryma_whipplei
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  Data_Nicole5
drwxr-xr-x  6 jhuang jhuang 4,0K Jun 18  2024  Data_Nicole5_77-92
drwxr-xr-x  3 jhuang jhuang 4,0K Jun 18  2024  Data_PaulBecher_Rotavirus
drwxr-xr-x 21 jhuang jhuang 4,0K Jun 18  2024  Data_Pietschmann_HCV_Amplicon_bigFile
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  Data_Piscine_Orthoreovirus_3_in_Brown_Trout
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  Data_Proteomics
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  Data_RNABioinformatics
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  Data_RNAKinetics
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  Data_R_courses
drwxr-xr-x  5 jhuang jhuang 4,0K Jun 18  2024  Data_SARS-CoV-2
drwxr-xr-x  9 jhuang jhuang 4,0K Jun 18  2024  Data_SARS-CoV-2_Genome_Announcement_PUBLISHED
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  Data_Seite
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  Data_Song_aggregate_sum
drwxr-xr-x  3 jhuang jhuang 4,0K Jun 18  2024  Data_Susanne_Amplicon_RdRp_orf1_2_re
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  Data_Tabea_RNASeq
drwxr-xr-x  5 jhuang jhuang 4,0K Jun 18  2024  Data_Thaiss1_Microarray_new
drwxr-xr-x 10 jhuang jhuang 4,0K Jun 18  2024  Data_Tintelnot_16S
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  Data_Wuenee_Plots
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  Data_Yang_Poster
drwxr-xr-x  4 jhuang jhuang 4,0K Jun 18  2024  Data_jupnote
drwxr-xr-x 21 jhuang jhuang 4,0K Jun 18  2024  Data_parainfluenza
drwxr-xr-x  9 jhuang jhuang 4,0K Jun 18  2024  Data_snakemake_recipe
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  Data_temp
drwxr-xr-x  3 jhuang jhuang 4,0K Jun 18  2024  Data_viGEN
drwxr-xr-x 19 jhuang jhuang 4,0K Jun 18  2024  Genomic_Data_Science
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  Learn_UGENE
drwxr-xr-x  5 jhuang jhuang 4,0K Jun 18  2024  MMcPaper
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  Manuscript_Epigenetics_Macrophage_Yersinia
drwxr-xr-x  6 jhuang jhuang 4,0K Jun 18  2024  Manuscript_RNAHiSwitch
drwxr-xr-x  4 jhuang jhuang 4,0K Jun 18  2024  MeDIP_Emilia_copy_DEL
drwxr-xr-x  5 jhuang jhuang 4,0K Jun 18  2024  Method_biopython
drwxr-xr-x  4 jhuang jhuang 4,0K Jun 18  2024  NGS
drwxr-xr-x  5 jhuang jhuang 4,0K Jun 18  2024  Okazaki-Seq_Processing
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  RNA-NGS_Analysis_modul3_NanoStringNorm
drwxr-xr-x  5 jhuang jhuang 4,0K Jun 18  2024  RNAConSLOptV1.2
drwxr-xr-x  9 jhuang jhuang 4,0K Jun 18  2024  RNAHeliCes
drwxr-xr-x 11 jhuang jhuang 4,0K Jun 18  2024  RNA_li_HeliCes
drwxr-xr-x 10 jhuang jhuang 4,0K Jun 18  2024  RNAliHeliCes
drwxr-xr-x 10 jhuang jhuang 4,0K Jun 18  2024  RNAliHeliCes_Relatedshapes_modified
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  R_refcard
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  R_DataCamp
drwxr-xr-x  3 jhuang jhuang 4,0K Jun 18  2024  R_cats_package
drwxr-xr-x  9 jhuang jhuang 4,0K Jun 18  2024  R_tutorials-master
drwxr-xr-x  7 jhuang jhuang 4,0K Jun 18  2024  SnakeChunks
drwxr-xr-x  6 jhuang jhuang 4,0K Jun 18  2024  align_4l_on_FJ705359
drwxr-xr-x  5 jhuang jhuang 4,0K Jun 18  2024  align_4p_on_FJ705359
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  assembly
drwxr-xr-x  6 jhuang jhuang 4,0K Jun 18  2024  bacto
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  bam2fastq_mapping_again
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  chipster
drwxr-xr-x  5 jhuang jhuang 4,0K Jun 18  2024  damian_GUI
drwxr-xr-x  4 jhuang jhuang 4,0K Jun 18  2024  enhancer-snakemake-demo
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  hg19_gene_annotations
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  interlab_comparison_DEL
drwxr-xr-x  5 jhuang jhuang 4,0K Jun 18  2024  my_flask
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  papers
drwxr-xr-x  6 jhuang jhuang 4,0K Jun 18  2024  pangenome-snakemake_zhaoc1
drwxr-xr-x 14 jhuang jhuang 4,0K Jun 18  2024  pyflow-epilogos
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  raw_data_rnaseq_Indra
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  test_raw_data_dnaseq
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024  test_raw_data_rnaseq
drwxr-xr-x  6 jhuang jhuang 4,0K Jun 18  2024  to_Francesco
drwxr-xr-x 36 jhuang jhuang 4,0K Jun 18  2024  ukepipe
drwxr-xr-x 15 jhuang jhuang 4,0K Jun 18  2024  ukepipe_nf
drwxr-xr-x 17 jhuang jhuang 4,0K Jun 18  2024  var_www_DjangoApp_mysite2_2023-05
-rwxr-xr-x  1 jhuang jhuang  59K Jun 18  2024  roentgenpass.pdf
-rwxr-xr-x  1 jhuang jhuang 9,1M Jun 18  2024  salmon_tx2gene_GRCh38.tsv
-rwxr-xr-x  1 jhuang jhuang 4,1K Jun 18  2024  salmon_tx2gene_chrHsv1.tsv
-rwxr-xr-x  1 jhuang jhuang 8,9K Jun 18  2024 'sample IDs_Lamprecht.xlsx'
-rwxr-xr-x  1 jhuang jhuang  30M Jun 18  2024  summarySCC_PM25.rds
-rwxr-xr-x  1 jhuang jhuang    0 Jun 18  2024  untitled.py
-rwxr-xr-x  1 jhuang jhuang  11M Jun 18  2024  tutorial-rnaseq.pdf
-rwxr-xr-x  1 jhuang jhuang 1,3K Jun 18  2024  x.log
-rwxr-xr-x  1 jhuang jhuang 381M Jun 18  2024  webapp.tar.gz
-rw-rw-r--  1 jhuang jhuang 8,4K Okt  9  2024  temp
-rw-rw-r--  1 jhuang jhuang 2,7K Okt  9  2024  temp2
drwxr-xr-x 51 jhuang jhuang  12K Feb 17 12:23  Data_Susanne_Amplicon_haplotype_analyses_RdRp_orf1_2_re
drwxr-xr-x  6 jhuang jhuang 4,0K Feb 17 12:42  Data_Susanne_WGS_unbiased

jhuang@WS-2290C:~/DATA_D$ ls -tlrh
total 56K
lrwxrwxrwx  1 jhuang jhuang   59 Apr 11  2024 Data_Soeren_RNA-seq_2023_PUBLISHING -> /media/jhuang/Elements/Data_Soeren_RNA-seq_2023_PUBLISHING/
lrwxrwxrwx  1 jhuang jhuang   32 Apr 11  2024 Data_Ute -> /media/jhuang/Elements/Data_Ute/
lrwxrwxrwx  1 jhuang jhuang   52 Apr 23  2024 Data_Marc_RNA-seq_Sepidermidis -> /media/jhuang/Titisee/Data_Marc_RNA-seq_Sepidermidis
drwxrwxr-x  2 jhuang jhuang 4,0K Mai  2  2024 Data_Patricia_Transposon
drwxrwxr-x  2 jhuang jhuang 4,0K Mai 29  2024 Books_DA_for_Life
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 18  2024 Data_Sven
-rw-rw-r--  1 jhuang jhuang 2,9K Jul 16  2024 Datasize_calculation_based_on_coverage.txt
drwxr-xr-x  6 jhuang jhuang 4,0K Jul 23  2024 Data_Paul_HD46_1-wt_resequencing
drwxrwxr-x  2 jhuang jhuang 4,0K Jul 26  2024 Data_Sanam_DAMIAN
drwxrwxr-x 26 jhuang jhuang  12K Jul 30  2024 Data_Tam_variant_calling
drwxrwxr-x  2 jhuang jhuang 4,0K Aug 26  2024 Data_Samira_Manuscripts
drwxrwxr-x  2 jhuang jhuang 4,0K Aug 27  2024 Data_Silvia_VoltRon_Debug
drwxrwxr-x 38 jhuang jhuang 4,0K Jun 10  2025 Data_Pietschmann_229ECoronavirus_Mutations_2024
drwxrwxr-x 23 jhuang jhuang 4,0K Jun 25  2025 Data_Pietschmann_229ECoronavirus_Mutations_2025
lrwxrwxrwx  1 jhuang jhuang   63 Nov 24 16:30 Data_Birthe_Svenja_RSV_Probe3_PUBLISHING -> /media/jhuang/Elements/Data_Birthe_Svenja_RSV_Probe3_PUBLISHING

jhuang@WS-2290C:~/DATA_E$ ls -tlrh
total 119M
drwxr-xr-x 10 jhuang jhuang 4,0K Apr 18  2019 j_huang_until_201904
drwxr-xr-x  2 jhuang jhuang 4,0K Apr 29  2019 Data_2019_April
drwxr-xr-x  2 jhuang jhuang 4,0K Mai 10  2019 Data_2019_May
drwxr-xr-x  2 jhuang jhuang 4,0K Jun 17  2019 Data_2019_June
drwxr-xr-x  2 jhuang jhuang 4,0K Jul 12  2019 Data_2019_July
drwxr-xr-x  3 jhuang jhuang 4,0K Aug 29  2019 Data_2019_August
drwxr-xr-x  3 jhuang jhuang 4,0K Sep  5  2019 Data_2019_September
drwxr-xr-x 11 jhuang jhuang 4,0K Apr 18  2023 Data_Song_RNASeq_PUBLISHED
drwxr-xr-x  7 jhuang jhuang 4,0K Okt 10  2023 Data_Laura_MP_RNASeq
drwxr-xr-x 22 jhuang jhuang  12K Nov  3  2023 Data_Nicole6_HEV_Swantje2
drwxr-xr-x 17 jhuang jhuang 4,0K Nov 13  2023 Data_Becher_Damian_Picornavirus_BovHepV
-rwxr-xr-x  1 jhuang jhuang 118M Nov 28  2023 bacteria_refseq.zip
drwxr-xr-x  3 jhuang jhuang 4,0K Nov 30  2023 bacteria_refseq
drwxr-xr-x  8 jhuang jhuang 4,0K Nov 30  2023 Data_Rotavirus
drwxr-xr-x  6 jhuang jhuang 4,0K Dez  6  2023 Data_Xiaobo_10x
drwx------ 17 jhuang jhuang 4,0K Feb  7  2025 Data_Becher_Damian_Picornavirus_BovHepV_INCOMPLETE_DEL

jhuang@WS-2290C:~/DATA_Intenso$ ls -ltrh
total 4,1G
drwxr-xr-x  15 jhuang jhuang 4,0K Mär 30  2015  HOME_FREIBURG_DEL
drwxr-xr-x   2 jhuang jhuang 4,0K Aug 12  2015  150810_M03701_0019_000000000-AFJFK
drwxr-xr-x   5 jhuang jhuang 4,0K Jan 31  2017  Data_Thaiss2_Microarray
drwxr-xr-x   9 jhuang jhuang 4,0K Apr 27  2017  VirtualBox_VMs_DEL
drwxr-xr-x   7 jhuang jhuang 4,0K Apr 27  2017 'VirtualBox VMs_DEL'
drwxr-xr-x   7 jhuang jhuang 4,0K Apr 27  2017 'VirtualBox VMs2_DEL'
drwxr-xr-x  16 jhuang jhuang 4,0K Mai 12  2017  websites
drwxr-xr-x   5 jhuang jhuang 4,0K Jun 29  2017  DATA
drwxr-xr-x 149 jhuang jhuang  36K Jun 30  2017  Data_Laura
drwxr-xr-x 149 jhuang jhuang  36K Jun 30  2017  Data_Laura_2
drwxr-xr-x   3 jhuang jhuang 4,0K Jun 30  2017  Data_Laura_3
drwxr-xr-x   7 jhuang jhuang 4,0K Jul 10  2017  galaxy_tools
drwxr-xr-x  45 jhuang jhuang  32K Jul 17  2017  Downloads2
drwxr-xr-x   3 jhuang jhuang 4,0K Jul 27  2017  Downloads
drwxr-xr-x   3 jhuang jhuang 4,0K Jul 28  2017  mom-baby_com_cn
drwxr-xr-x   3 jhuang jhuang 4,0K Aug  8  2017 'VirtualBox VMs2'
drwxr-xr-x   3 jhuang jhuang 4,0K Aug  9  2017  VirtualBox_VMs
drwxr-xr-x   3 jhuang jhuang 4,0K Aug 11  2017  CLC_Data
drwxr-xr-x   6 jhuang jhuang  12K Aug 14  2017  Work_Dir2
drwxr-xr-x   7 jhuang jhuang 4,0K Aug 15  2017  Work_Dir2_SGE
drwxr-xr-x  19 jhuang jhuang 4,0K Aug 24  2017  Data_SPANDx1_Kpneumoniae_vs_Assembly1
drwxr-xr-x   3 jhuang jhuang 4,0K Aug 24  2017  MauveOutput
drwxr-xr-x   3 jhuang jhuang 4,0K Aug 31  2017  Fastqs
drwxr-xr-x  20 jhuang jhuang 4,0K Sep  7  2017  Data_Anna3_VRE_Ausbruch
drwxr-xr-x   8 jhuang jhuang 4,0K Sep 19  2017  Work_Dir_mock_broad_mockinput
drwxr-xr-x   8 jhuang jhuang 4,0K Sep 19  2017  Work_Dir_dM_broad_mockinput
drwxr-xr-x   4 jhuang jhuang 4,0K Okt  6  2017  Data_Anna8_RNASeq_static_shake_deprecated
drwxr-xr-x  24 jhuang jhuang 4,0K Okt  9  2017  PENDRIVE_cont
drwxr-xr-x   8 jhuang jhuang 4,0K Okt 23  2017  Work_Dir_WAP_broad_mockinput
drwxr-xr-x  10 jhuang jhuang 4,0K Okt 23  2017  Work_Dir_WAC_broad_mockinput
drwxr-xr-x  11 jhuang jhuang 4,0K Okt 23  2017  Work_Dir_dP_broad_mockinput
drwxr-xr-x  52 jhuang jhuang 4,0K Nov  8  2017  Data_Nicole10_16S_interlab
drwxr-xr-x   6 jhuang jhuang 4,0K Dez  6  2017  PAPERS
drwxr-xr-x  14 jhuang jhuang  16K Dez 15  2017  TB
drwxr-xr-x   5 jhuang jhuang 4,0K Dez 19  2017  Data_Anna4_SNP
drwxr-xr-x  11 jhuang jhuang 4,0K Jan 16  2018  Data_Carolin1_16S
drwxr-xr-x   2 jhuang jhuang 4,0K Jan 22  2018  ChipSeq_Raw_Data3_171009_NB501882_0024_AHNGTYBGX3
-rw-r--r--   1 jhuang jhuang 4,0G Jan 23  2018  m_aepfelbacher_DEL.zip
drwxr-xr-x   7 jhuang jhuang 4,0K Jan 24  2018  Data_Anna7_RNASeq_Cytoscape
drwxr-xr-x   3 jhuang jhuang 4,0K Jan 24  2018  Data_Nicole9_Hund_Katze_Mega
drwxr-xr-x  39 jhuang jhuang  20K Jan 28  2018  Data_Anna2_CO6114
drwxr-xr-x   3 jhuang jhuang 4,0K Jan 28  2018  Data_Nicole3_TH17_orig
drwxr-xr-x  27 jhuang jhuang  28K Jan 28  2018  Data_Nicole1_Tropheryma_whipplei
drwxr-xr-x  16 jhuang jhuang 4,0K Jan 30  2018  results_K27
drwxr-xr-x   2 jhuang jhuang 4,0K Feb 19  2018 'VirtualBox VMs'
drwxr-xr-x  28 jhuang jhuang  12K Feb 27  2018  Data_Anna6_RNASeq
drwxr-xr-x  17 jhuang jhuang  12K Mär  1  2018  Data_Anna1_1585_RNAseq
drwxr-xr-x  21 jhuang jhuang 4,0K Mär  7  2018  Data_Thaiss1_Microarray
drwxr-xr-x  25 jhuang jhuang  12K Mär 27  2018  Data_Nicole7_Anelloviruses_Polyomavirus
drwxr-xr-x  13 jhuang jhuang 4,0K Mai 22  2018  Data_Nina1_Nicole5_1-76
drwxr-xr-x  11 jhuang jhuang 4,0K Mai 22  2018  Data_Nina1_merged
drwxr-xr-x  32 jhuang jhuang 4,0K Jun 14  2018  Data_Nicole8_Lamprecht
drwxr-xr-x  40 jhuang jhuang  16K Jul  5  2018  Data_Anna5_SNP
drwxr-xr-x  35 jhuang jhuang 4,0K Okt 12  2018  chipseq
drwxr-xr-x 107 jhuang jhuang  76K Mai 18  2019  Downloads_DEL
drwxr-xr-x   7 jhuang jhuang 4,0K Mär 17  2020  Data_Gagliani2_enriched_16S
drwxr-xr-x  17 jhuang jhuang 4,0K Mär 17  2020  Data_Gagliani1_18S_16S
drwxr-xr-x   2 jhuang jhuang 4,0K Apr  2  2020  m_aepfelbacher
drwxr-xr-x   4 jhuang jhuang 4,0K Feb 17 12:38  Data_Susanne_WGS_3amplicons

jhuang@WS-2290C:/media/jhuang/Titisee$ ls -tlrh
total 3,5G
drwxrwxrwx 1 jhuang jhuang    0 Dez 19  2017  Data_Anna4_SNP
drwxrwxrwx 1 jhuang jhuang 4,0K Jan 24  2018  Data_Anna5_SNP_rsync_error
-rwxrwxrwx 1 jhuang jhuang 9,9K Mär 21  2018  TRASH
drwxrwxrwx 1 jhuang jhuang  20K Mär 28  2018  Data_Nicole6_HEV_4_SNP_calling_PE_DEL
drwxrwxrwx 1 jhuang jhuang 4,0K Mai 22  2018  Data_Nina1_Nicole7
drwxrwxrwx 1 jhuang jhuang 8,0K Mai 24  2018  Data_Nicole6_HEV_4_SNP_calling_SE_DEL
-rwxrwxrwx 1 jhuang jhuang 3,5G Jun 14  2018  180119_M03701_0115_000000000-BFG46.zip
drwxrwxrwx 1 jhuang jhuang 4,0K Jul 10  2018  Data_Nicole10_16S_interlab_PUBLISHED
drwxrwxrwx 1 jhuang jhuang 4,0K Jul 10  2018  Anna11_assemblies
drwxrwxrwx 1 jhuang jhuang 4,0K Jul 11  2018  Anna11_trees
drwxrwxrwx 1 jhuang jhuang 4,0K Jul 24  2018  Data_Nicole6_HEV_new_orig_fastqs
drwxrwxrwx 1 jhuang jhuang 4,0K Nov 23  2018  Data_Anna9_OXA-48_or_OXA-181
drwxrwxrwx 1 jhuang jhuang 4,0K Feb 15  2019  bengal_results_v1_2018
-rwxrwxrwx 1 jhuang jhuang 9,8M Mär 22  2019  DO.pdf
drwxrwxrwx 1 jhuang jhuang 4,0K Mai  6  2019  damian_DEL
drwxrwxrwx 1 jhuang jhuang    0 Mai 20  2019  MAGpy_db
drwxrwxrwx 1 jhuang jhuang    0 Aug  3  2019  UGENE_v1_32_data_cistrome
drwxrwxrwx 1 jhuang jhuang 4,0K Aug  3  2019  UGENE_v1_32_data_ngs_classification
drwxrwxrwx 1 jhuang jhuang  52K Okt 25  2019  Data_Nicole6_HEV_Swantje
drwxrwxrwx 1 jhuang jhuang 8,0K Okt 25  2019  Data_Nico_Gagliani
drwxrwxrwx 1 jhuang jhuang 4,0K Mär 30  2020  GAMOLA2_prototyp
drwxrwxrwx 1 jhuang jhuang 8,0K Mär 31  2020  Thomas_methylation_EPIC_DO
drwxrwxrwx 1 jhuang jhuang 8,0K Jun 15  2020  Data_Nicola_Schaltenberg
drwxrwxrwx 1 jhuang jhuang  36K Jun 25  2020  Data_Nicola_Schaltenberg_PICRUSt
drwxrwxrwx 1 jhuang jhuang  12K Jan 25  2021  HOME_FREIBURG
drwxrwxrwx 1 jhuang jhuang 4,0K Okt 13  2021  Data_Francesco_16S
drwxrwxrwx 1 jhuang jhuang 4,0K Jun 14  2022  3rd_party
drwxrwxrwx 1 jhuang jhuang 4,0K Jul 29  2022  ConsPred_prokaryotic_genome_annotation
drwxrwxrwx 1 jhuang jhuang 4,0K Aug  2  2022 'System Volume Information'
drwxrwxrwx 1 jhuang jhuang    0 Sep 16  2022  damian_v201016
drwxrwxrwx 1 jhuang jhuang  36K Jan 12  2023  Data_Holger_VRE
drwxrwxrwx 1 jhuang jhuang  32K Feb  1  2023  Data_Holger_Pseudomonas_aeruginosa_SNP
drwxrwxrwx 1 jhuang jhuang 4,0K Sep  5  2023  Eigene_Ordner_HR
drwxrwxrwx 1 jhuang jhuang  24K Sep  6  2023  GAMOLA2
drwxrwxrwx 1 jhuang jhuang  24K Sep 27  2023  Data_Anastasia_RNASeq
drwxrwxrwx 1 jhuang jhuang  24K Okt 20  2023  Data_Amir_PUBLISHED
drwxrwxrwx 1 jhuang jhuang  44K Apr 25  2024  Data_Marc_RNA-seq_Sepidermidis
drwxrwxrwx 1 jhuang jhuang 4,0K Sep 23  2024 '$RECYCLE.BIN'
drwxrwxrwx 1 jhuang jhuang 4,0K Sep 23  2024  Data_Xiaobo_10x_3
drwxrwxrwx 1 jhuang jhuang  24K Nov 28  2024  Data_Tam_DNAseq_2023_Comparative_ATCC19606_AYE_ATCC17978
drwxrwxrwx 1 jhuang jhuang  48K Dez 19  2024  Data_Holger_S.epidermidis_short
-rwxrwxrwx 1 jhuang jhuang   31 Feb  4  2025  TEMP
drwxrwxrwx 1 jhuang jhuang  12K Aug 22 11:44  Data_Holger_S.epidermidis_long

jhuang@WS-2290C:/media/jhuang/Elements(Denise_ChIPseq)$ ls -tlrh
total 11M
drwxr-xr-x 1 jhuang jhuang 4,0K Jun  7  2019  Data_Denise_LTtrunc_H3K27me3_2_results_DEL
drwxr-xr-x 1 jhuang jhuang 4,0K Jun  7  2019  Data_Denise_LTtrunc_H3K4me3_2_results_DEL
drwxr-xr-x 1 jhuang jhuang  28K Aug 26  2019  Data_Anna12_HAPDICS_final_not_finished_DEL
drwxr-xr-x 1 jhuang jhuang 4,0K Okt 24  2019  m_aepfelbacher_DEL
drwxr-xr-x 1 jhuang jhuang  20K Jan 14  2020  Data_Damian
drwxr-xr-x 1 jhuang jhuang 4,0K Jan 25  2020  ST772_DEL
drwxr-xr-x 1 jhuang jhuang 160K Jan 25  2020  ALL_trimmed_part_DEL
drwxr-xr-x 1 jhuang jhuang    0 Mär 30  2020  Data_Denise_ChIPSeq_Protocol1
drwxr-xr-x 1 jhuang jhuang  44K Mai 19  2020  Data_Pietschmann_HCV_Amplicon
drwxr-xr-x 1 jhuang jhuang  60K Jun 26  2020  Data_Nicole6_HEV_ownMethod_new
-rwxr-xr-x 1 jhuang jhuang 2,5M Aug  5  2020  HD04-1.fasta
drwxr-xr-x 1 jhuang jhuang 4,0K Mai 31  2021  RNAHiSwitch_
drwxr-xr-x 1 jhuang jhuang 4,0K Mai 31  2021  RNAHiSwitch__
drwxr-xr-x 1 jhuang jhuang 8,0K Jun 17  2021  RNAHiSwitch___
drwxr-xr-x 1 jhuang jhuang 4,0K Jun 25  2021  RNAHiSwitch_paper_
drwxr-xr-x 1 jhuang jhuang    0 Jul  7  2021  RNAHiSwitch_milestone1_DELETED
-rwxr-xr-x 1 jhuang jhuang 7,2M Jul  7  2021  RNAHiSwitch_paper.tar.gz
drwxr-xr-x 1 jhuang jhuang 4,0K Jul 12  2021  RNAHiSwitch_paper_DELETED
drwxr-xr-x 1 jhuang jhuang  12K Jul 12  2021  RNAHiSwitch_milestone1
drwxr-xr-x 1 jhuang jhuang 4,0K Aug 23  2021  RNAHiSwitch_paper
drwxr-xr-x 1 jhuang jhuang 4,0K Sep 24  2021  Ute_RNASeq_results
drwxr-xr-x 1 jhuang jhuang 4,0K Sep 24  2021  Ute_miRNA_results_38
drwxr-xr-x 1 jhuang jhuang  88K Okt 27  2021  RNAHiSwitch
drwxr-xr-x 1 jhuang jhuang  48K Mär 31  2022  Data_HepE_Freiburg_PUBLISHED
drwxr-xr-x 1 jhuang jhuang 4,0K Jun  1  2022  Data_INTENSO_2022-06
drwxr-xr-x 1 jhuang jhuang    0 Sep 14  2022 '$RECYCLE.BIN'
drwxr-xr-x 1 jhuang jhuang 4,0K Sep 14  2022 'System Volume Information'
drwxr-xr-x 1 jhuang jhuang 4,0K Dez  7  2022  Data_Anna_Mixta_hanseatica_PUBLISHED
-rwxr-xr-x 1 jhuang jhuang  33K Dez  9  2022  coi_disclosure.docx
drwxr-xr-x 1 jhuang jhuang  20K Feb  8  2023  Data_Jingang
drwxr-xr-x 1 jhuang jhuang 4,0K Mai 30  2023  Data_Arck_16S_MMc_PUBLISHED
drwxr-xr-x 1 jhuang jhuang 4,0K Jun  5  2023  Data_Laura_ChIPseq_GSE120945
drwxr-xr-x 1 jhuang jhuang  80K Jun  5  2023  Data_Nicole6_HEV_ownMethod
drwxr-xr-x 1 jhuang jhuang 8,0K Jul  5  2023  Data_Susanne_16S_re_UNPUBLISHED *
drwxr-xr-x 1 jhuang jhuang 4,0K Okt 12  2023  Data_Denise_ChIPSeq_Protocol2
drwxr-xr-x 1 jhuang jhuang 4,0K Okt 20  2023  Data_Caroline_RNAseq_wt_timecourse
drwxr-xr-x 1 jhuang jhuang 4,0K Okt 20  2023  Data_Caroline_RNAseq_brain_organoids
drwxr-xr-x 1 jhuang jhuang  20K Okt 20  2023  Data_Amir_PUBLISHED_DEL
drwxr-xr-x 1 jhuang jhuang 4,0K Nov 24  2023  Data_download_virus_fam
drwxr-xr-x 1 jhuang jhuang  12K Feb 22  2024  Data_Gunnar_Yersiniomics_COPYFAILED_DEL
drwxr-xr-x 1 jhuang jhuang  20K Feb 27  2024  Data_Paul_and_Marc_Epidome_batch3
-rwxr-xr-x 1 jhuang jhuang 3,0K Okt 30  2024  ifconfig_hamm.txt
drwxr-xr-x 1 jhuang jhuang 8,0K Apr  8  2025  Data_Soeren_2023_PUBLISHING
drwxr-xr-x 1 jhuang jhuang  28K Nov 24 13:34  Data_Birthe_Svenja_RSV_Probe3_PUBLISHING
drwxr-xr-x 1 jhuang jhuang  20K Jan 13 17:46  Data_Ute
drwxr-xr-x 1 jhuang jhuang  12K Feb 17 12:48  Data_Susanne_16S_UNPUBLISHED *

jhuang@WS-2290C:/media/jhuang/Seagate Expansion Drive(HOffice)$ ls -tlrh
total 19M
-rwxrwxrwx 1 jhuang jhuang 550K Jan  8  2015  SeagateExpansion.ico
-rwxrwxrwx 1 jhuang jhuang   38 Mär 27  2015  Autorun.inf
-rwxrwxrwx 2 jhuang jhuang  18M Mai  4  2017  Start_Here_Win.exe
-rwxrwxrwx 1 jhuang jhuang 1,1M Jul  7  2017  Warranty.pdf
drwxrwxrwx 1 jhuang jhuang    0 Jan  9  2018  Start_Here_Mac.app
drwxrwxrwx 1 jhuang jhuang    0 Jan  9  2018  Seagate
drwxrwxrwx 1 jhuang jhuang    0 Jun  5  2024  HomeOffice_DIR (Data_Anna_HAPDICS_RNASeq, From_Samsung_T5)
drwxrwxrwx 1 jhuang jhuang 4,0K Jun 17  2024  DATA_COPY_FROM_178528 (copy_and_clean.sh, logfile_jhuang.log, jhuang)
drwxrwxrwx 1 jhuang jhuang    0 Sep  9 10:41 'System Volume Information'
drwxrwxrwx 1 jhuang jhuang    0 Sep  9 10:41 '$RECYCLE.BIN'

jhuang@WS-2290C:/media/jhuang/Elements(Anna_C.arnes)$ ls -trlh
total 236K
drwxrwxrwx 1 jhuang jhuang 8,0K Nov 14  2018  Data_Swantje_HEV_using_viral-ngs
drwxrwxrwx 1 jhuang jhuang    0 Dez  4  2018  VIPER_static_DEL
drwxrwxrwx 1 jhuang jhuang 4,0K Apr  4  2019  Data_Nicole6_HEV_Swantje1_blood
drwxrwxrwx 1 jhuang jhuang  24K Apr  5  2019  Data_Nicole6_HEV_benchmark
drwxrwxrwx 1 jhuang jhuang  20K Mär 12  2020  Data_Denise_RNASeq_GSE79958
drwxrwxrwx 1 jhuang jhuang 8,0K Jan 11  2022  Data_16S_Leonie_from_Nico_Gaglianis
drwxrwxrwx 1 jhuang jhuang 8,0K Jul 29  2022  Fastqs_19-21
drwxrwxrwx 1 jhuang jhuang 4,0K Aug  2  2022 'System Volume Information'
drwxrwxrwx 1 jhuang jhuang 8,0K Sep 23  2022  Data_Luise_Epidome_test
drwxrwxrwx 1 jhuang jhuang  48K Sep 27  2023  Data_Anna_C.acnes_PUBLISHED
drwxrwxrwx 1 jhuang jhuang  24K Dez  6  2023  Data_Denise_LT_DNA_Bindung
drwxrwxrwx 1 jhuang jhuang 4,0K Jan  9  2024  Data_Denise_LT_K331A_RNASeq
drwxrwxrwx 1 jhuang jhuang  12K Jan 10  2024  Data_Luise_Epidome_batch1
drwxrwxrwx 1 jhuang jhuang  28K Feb 26  2024  Data_Luise_Pseudomonas_aeruginosa_PUBLISHED
drwxrwxrwx 1 jhuang jhuang  28K Feb 27  2024  Data_Luise_Epidome_batch2
drwxrwxrwx 1 jhuang jhuang 4,0K Sep  5  2024  picrust2_out_2024_2
drwxrwxrwx 1 jhuang jhuang 4,0K Mär 11  2025 '$RECYCLE.BIN'

jhuang@WS-2290C:/media/jhuang/Seagate Expansion Drive(DATA_COPY_FROM_hamburg)$ ls -tlrh
total 19M
-rwxrwxrwx 1 jhuang jhuang   33 Feb 21  2018 Autorun.inf
-rwxrwxrwx 2 jhuang jhuang  18M Jun 21  2019 Start_Here_Win.exe
-rwxrwxrwx 1 jhuang jhuang 1,6M Jul  6  2020 Warranty.pdf
drwxrwxrwx 1 jhuang jhuang    0 Mär 10  2021 Start_Here_Mac.app
drwxrwxrwx 1 jhuang jhuang    0 Mär 10  2021 Seagate
drwxrwxrwx 1 jhuang jhuang  12K Jun 29  2022 DATA_COPY_TRANSFER_INCOMPLETE_DEL
drwxrwxrwx 1 jhuang jhuang 4,0K Dez 16  2024 DATA_COPY_FROM_hamburg

jhuang@WS-2290C:/media/jhuang/Seagate Expansion Drive(Seagate_1)$ ls -trlh
total 104G
drwxr-xr-x 1 jhuang jhuang 4,0K Okt  3  2013  RNA_seq_analysis_tools_2013
drwxr-xr-x 1 jhuang jhuang    0 Feb 28  2018  Data_Laura0
drwxr-xr-x 1 jhuang jhuang 8,0K Sep  6  2018  Data_Petra_Arck
drwxr-xr-x 1 jhuang jhuang 4,0K Sep 14  2018  Data_Martin_mycoplasma
drwxr-xr-x 1 jhuang jhuang 8,0K Dez  5  2018  chromhmm-enhancers
drwxr-xr-x 1 jhuang jhuang 4,0K Jan 15  2019  ChromHMM_Dir
drwxr-xr-x 1 jhuang jhuang 4,0K Jan 18  2019  Data_Denise_sT_H3K4me3
drwxr-xr-x 1 jhuang jhuang 4,0K Jan 18  2019  Data_Denise_sT_H3K27me3
drwxr-xr-x 1 jhuang jhuang    0 Feb 13  2019  Start_Here_Mac.app
drwxr-xr-x 1 jhuang jhuang    0 Feb 13  2019  Seagate
drwxr-xr-x 1 jhuang jhuang 4,0K Feb 19  2019  Data_Nicole16_parapoxvirus
-rwxr-xr-x 1 jhuang jhuang  39G Aug 20  2019  Project_h_rohde_Susanne_WGS_unbiased_DEL.zip
drwxr-xr-x 1 jhuang jhuang 4,0K Nov 11  2019  Data_Denise_ChIPSeq_Protocol1
drwxr-xr-x 1 jhuang jhuang 8,0K Nov 13  2019  Data_ENNGS_pathogen_detection_pipeline_comparison
drwxr-xr-x 1 jhuang jhuang 4,0K Feb 18  2020  j_huang_201904_202002
-rwxr-xr-x 1 jhuang jhuang  112 Mär  2  2020  Data_Laura_ChIPseq_GSE120945
drwxr-xr-x 1 jhuang jhuang 8,0K Mär 26  2020  batch_200314_incomplete
-rwxr-xr-x 1 jhuang jhuang  65G Mär 26  2020  m_aepfelbacher.zip
drwxr-xr-x 1 jhuang jhuang    0 Mär 26  2020  m_error_DEL
drwxr-xr-x 1 jhuang jhuang 4,0K Mär 28  2020  batch_200325
drwxr-xr-x 1 jhuang jhuang 4,0K Mär 28  2020  batch_200319
drwxr-xr-x 1 jhuang jhuang 4,0K Mär 30  2020  GAMOLA2_prototyp
drwxr-xr-x 1 jhuang jhuang 4,0K Jun 22  2020  Data_Nicola_Gagliani
drwxr-xr-x 1 jhuang jhuang 4,0K Sep  3  2020  2017-18_raw_data
drwxr-xr-x 1 jhuang jhuang 1,2M Sep 11  2020  Data_Arck_MeDIP
drwxr-xr-x 1 jhuang jhuang 4,0K Okt 16  2020  trimmed
drwxr-xr-x 1 jhuang jhuang 4,0K Dez 23  2020  Data_Nicole_16S_Christmas_2020_2
drwxr-xr-x 1 jhuang jhuang 4,0K Jan 14  2021  j_huang_202007_202012
drwxr-xr-x 1 jhuang jhuang 4,0K Jan 15  2021  Data_Nicole_16S_Christmas_2020
drwxr-xr-x 1 jhuang jhuang 184K Jan 18  2021  Downloads_2021-01-18_DEL
drwxr-xr-x 1 jhuang jhuang 4,0K Jan 28  2021  Data_Laura_plasmid
drwxr-xr-x 1 jhuang jhuang 4,0K Mär 18  2021  Data_Laura_16S_2_re
drwxr-xr-x 1 jhuang jhuang 8,0K Mär 22  2021  Data_Laura_16S_2
drwxr-xr-x 1 jhuang jhuang 4,0K Mär 22  2021  Data_Laura_16S_2_re_
drwxr-xr-x 1 jhuang jhuang 8,0K Mär 23  2021  Data_Laura_16S_merged
drwxr-xr-x 1 jhuang jhuang  32K Nov  7  2022  Downloads_DEL
drwxr-xr-x 1 jhuang jhuang  12K Nov  7  2022  Data_Laura_16S
drwxr-xr-x 1 jhuang jhuang  76K Nov  9  2023  Data_Anna12_HAPDICS_final
drwxr-xr-x 1 jhuang jhuang    0 Dez  4  2023 '$RECYCLE.BIN'
drwxr-xr-x 1 jhuang jhuang 4,0K Dez  4  2023 'System Volume Information'

jhuang@WS-2290C:/media/jhuang/Seagate Expansion Drive(Seagate_2)$ ls -trlh
total 70G
drwxr-xr-x 1 jhuang jhuang 4,0K Jan  5  2017  Data_Nicole4_TH17
-rwxr-xr-x 1 jhuang jhuang  18M Feb  9  2018  Start_Here_Win.exe
-rwxr-xr-x 1 jhuang jhuang   33 Feb 21  2018  Autorun.inf
-rwxr-xr-x 1 jhuang jhuang 1,2M Jul 26  2018  Warranty.pdf
drwxr-xr-x 1 jhuang jhuang    0 Feb 13  2019  Start_Here_Mac.app
drwxr-xr-x 1 jhuang jhuang    0 Feb 13  2019  Seagate
drwxr-xr-x 1 jhuang jhuang 4,0K Dez 20  2019  Data_Denise_RNASeq_trimmed_DEL
drwxr-xr-x 1 jhuang jhuang 4,0K Jan 25  2020  HD12
drwxr-xr-x 1 jhuang jhuang 4,0K Jan 25  2020  Qi_panGenome
drwxr-xr-x 1 jhuang jhuang  44K Jan 25  2020  ALL
drwxr-xr-x 1 jhuang jhuang    0 Feb 14  2020  fastq_HPI_bw_2019_08_and_2020_02
-rwxr-xr-x 1 jhuang jhuang  19K Mär 12  2020  f1_R1_link.sh
-rwxr-xr-x 1 jhuang jhuang  19K Mär 12  2020  f1_R2_link.sh
drwxr-xr-x 1 jhuang jhuang  28K Mär 19  2020  rtpd_files
-rwxr-xr-x 1 jhuang jhuang  65G Apr  2  2020  m_aepfelbacher.zip
drwxr-xr-x 1 jhuang jhuang 4,0K Apr 20  2020  Data_Nicole_16S_Hamburg_Odense_Cornell_Muenster
drwxr-xr-x 1 jhuang jhuang 8,0K Apr 21  2020  HyAsP_incomplete_genomes
drwxr-xr-x 1 jhuang jhuang 4,0K Apr 25  2020  HyAsP_normal_sampled_input
drwxr-xr-x 1 jhuang jhuang 8,0K Apr 28  2020  HyAsP_complete_genomes
-rwxr-xr-x 1 jhuang jhuang 176M Mai  8  2020  video.zip
-rwxr-xr-x 1 jhuang jhuang 6,9K Jun  2  2020  sam2bedgff.pl
-rwxr-xr-x 1 jhuang jhuang 5,5K Jul  7  2020  HD04.infection.hS_vs_HD04.nose.hS_annotated_degenes.xls
drwxr-xr-x 1 jhuang jhuang  44K Jul  9  2020  ALL83
drwxr-xr-x 1 jhuang jhuang  20K Jul  9  2020  Data_Pietschmann_RSV_Probe_PUBLISHED
drwxr-xr-x 1 jhuang jhuang 8,0K Jul 27  2020  HyAsP_normal
drwxr-xr-x 1 jhuang jhuang 4,0K Jul 28  2020  Data_Manthey_16S
drwxr-xr-x 1 jhuang jhuang 8,0K Jul 29  2020  rtpd_files_DEL
drwxr-xr-x 1 jhuang jhuang  20K Aug 11  2020  HyAsP_bold
drwxr-xr-x 1 jhuang jhuang  44K Aug 17  2020  Data_HEV
drwxr-xr-x 1 jhuang jhuang 4,0K Sep 29  2020  Seq_VRE_hybridassembly
drwxr-xr-x 1 jhuang jhuang  12K Nov 11  2020  Data_Anna12_HAPDICS_raw_data_shovill_prokka
drwxr-xr-x 1 jhuang jhuang  12K Aug 10  2021  Data_Anna_HAPDICS_WGS_ALL
drwxr-xr-x 1 jhuang jhuang  20K Aug 10  2021  Data_HEV_Freiburg_2020
drwxr-xr-x 1 jhuang jhuang  20K Okt 27  2021  Data_Nicole_HDV_Recombination_PUBLISHED
-rwxr-xr-x 1 jhuang jhuang 905K Feb  8  2022  s_hero2x
-rwxr-xr-x 1 jhuang jhuang 5,5G Feb 25  2022  201030_M03701_0207_000000000-J57B4.zip
-rwxr-xr-x 1 jhuang jhuang 4,9K Mär 21  2022  README
-rwxr-xr-x 1 jhuang jhuang 4,9K Mär 21  2022 'README(1)'
-rwxr-xr-x 1 jhuang jhuang  848 Mär 28  2022  dna2.fasta.fai
-rwxr-xr-x 1 jhuang jhuang  17K Mär 28  2022  91.pep
-rwxr-xr-x 1 jhuang jhuang 9,1K Mär 28  2022  91.orf
-rwxr-xr-x 1 jhuang jhuang  222 Mär 28  2022  91.orf.fai
-rwxr-xr-x 1 jhuang jhuang 1,1M Mär 31  2022  dgaston-dec-06-2012-121211124858-phpapp01.pdf
-rwxr-xr-x 1 jhuang jhuang 5,2K Apr  4  2022  tileshop.fcgi
-rwxr-xr-x 1 jhuang jhuang 765K Apr  4  2022  ppat.1009304.s016.tif
-rwxr-xr-x 1 jhuang jhuang 4,1K Mai  2  2022  sequence.txt
-rwxr-xr-x 1 jhuang jhuang 4,0K Mai  2  2022 'sequence(1).txt'
-rwxr-xr-x 1 jhuang jhuang 3,7K Mai 23  2022  GSE128169_series_matrix.txt.gz
-rwxr-xr-x 1 jhuang jhuang 4,0K Mai 23  2022  GSE128169_family.soft.gz
drwxr-xr-x 1 jhuang jhuang  40K Mär 20  2023  Data_Anna_HAPDICS_RNASeq
drwxr-xr-x 1 jhuang jhuang 1,3M Apr  4  2023  Data_Christopher_MeDIP_MMc_PUBLISHED
drwxr-xr-x 1 jhuang jhuang 8,0K Jun 28  2023  Data_Gunnar_Yersiniomics_IMCOMPLETE_DEL
drwxr-xr-x 1 jhuang jhuang  28K Feb 12  2024  Data_Denise_RNASeq
drwxr-xr-x 1 jhuang jhuang 4,0K Apr  5  2024 'System Volume Information'
drwxr-xr-x 1 jhuang jhuang    0 Apr  5  2024 '$RECYCLE.BIN'

jhuang@WS-2290C:/media/jhuang/Elements(An14_RNAs)$ ls -tlrh
total 284K
drwxr-xr-x 1 jhuang jhuang 8,0K Aug  7  2017  Data_Anna10_RP62A
drwxr-xr-x 1 jhuang jhuang 4,0K Jun 15  2018  Data_Nicole12_16S_Kluwe_Bunders
drwxr-xr-x 1 jhuang jhuang 4,0K Nov 30  2018  chromhmm-enhancers
drwxr-xr-x 1 jhuang jhuang    0 Apr  1  2019  Data_Denise_sT_Methylation
drwxr-xr-x 1 jhuang jhuang    0 Apr  1  2019  Data_Denise_LTtrunc_Methylation
drwxr-xr-x 1 jhuang jhuang  12K Apr 29  2019  Data_16S_arckNov
drwxr-xr-x 1 jhuang jhuang 4,0K Mai 29  2019  Data_Tabea_RNASeq
-rwxr-xr-x 1 jhuang jhuang 4,6K Mai 29  2019  nr_gz_README
drwxr-xr-x 1 jhuang jhuang 4,0K Jun  5  2019  j_huang_raw_fq
drwxr-xr-x 1 jhuang jhuang    0 Jun  7  2019 'System Volume Information'
drwxr-xr-x 1 jhuang jhuang    0 Jun  7  2019 '$RECYCLE.BIN'
drwxr-xr-x 1 jhuang jhuang  36K Jun 18  2019  host_refs
drwxr-xr-x 1 jhuang jhuang    0 Jun 18  2019  Vraw
drwxr-xr-x 1 jhuang jhuang  68K Jul 29  2019  Data_Susanne_Amplicon_RdRp_orf1_2 *
drwxr-xr-x 1 jhuang jhuang 4,0K Aug  6  2019  tmp
drwxr-xr-x 1 jhuang jhuang  28K Sep  4  2020  Data_RNA188_Paul_Becher
drwxr-xr-x 1 jhuang jhuang 4,0K Nov  3  2020  Data_ChIPSeq_Laura
drwxr-xr-x 1 jhuang jhuang  12K Mai  7  2021  Data_16S_arckNov_review_PUBLISHED
drwxr-xr-x 1 jhuang jhuang 8,0K Mai  7  2021  Data_16S_arckNov_re
drwxr-xr-x 1 jhuang jhuang  20K Mai 25  2021  Fastqs
drwxr-xr-x 1 jhuang jhuang 4,0K Aug  9  2021  Data_Tabea_RNASeq_submission
drwxr-xr-x 1 jhuang jhuang 4,0K Aug 27  2021  Data_Anna_Cutibacterium_acnes_DEL
drwxr-xr-x 1 jhuang jhuang    0 Sep 16  2021  Data_Silvia_RNASeq_SUBMISSION
drwxr-xr-x 1 jhuang jhuang 4,0K Feb  9  2022  Data_Hannes_ChIPSeq
drwxr-xr-x 1 jhuang jhuang 4,0K Jul  5  2022  Data_Anna14_RNASeq_to_be_DEL
drwxr-xr-x 1 jhuang jhuang  40K Dez 15  2022  Data_Pietschmann_RSV_Probe2_PUBLISHED
drwxr-xr-x 1 jhuang jhuang    0 Dez 16  2022  Data_Holger_Klebsiella_pneumoniae_SNP_PUBLISHING
drwxr-xr-x 1 jhuang jhuang 4,0K Jun 29  2023  Data_Anna14_RNASeq_plus_public

jhuang@WS-2290C:/media/jhuang/Elements(Indra_HAPDICS)$ ls -trlh
total 452K
drwxrwxrwx 1 jhuang jhuang  20K Jul  3  2018  Data_Anna11_Sepdermidis_DEL
drwxrwxrwx 1 jhuang jhuang  20K Jul 12  2018  HD15_without_10
drwxrwxrwx 1 jhuang jhuang  12K Jul 12  2018  HD31
drwxrwxrwx 1 jhuang jhuang  20K Jul 12  2018  HD33
drwxrwxrwx 1 jhuang jhuang  20K Jul 12  2018  HD39
drwxrwxrwx 1 jhuang jhuang  20K Jul 12  2018  HD43
drwxrwxrwx 1 jhuang jhuang  20K Jul 12  2018  HD46
drwxrwxrwx 1 jhuang jhuang  20K Jul 12  2018  HD15_with_10
drwxrwxrwx 1 jhuang jhuang  12K Jul 13  2018  HD26
drwxrwxrwx 1 jhuang jhuang  20K Jul 13  2018  HD59
drwxrwxrwx 1 jhuang jhuang  12K Jul 13  2018  HD25
drwxrwxrwx 1 jhuang jhuang  20K Jul 16  2018  HD21
drwxrwxrwx 1 jhuang jhuang  20K Jul 17  2018  HD17
drwxrwxrwx 1 jhuang jhuang  24K Sep 24  2018  HD04
drwxrwxrwx 1 jhuang jhuang  20K Mär  5  2019  Data_Anna11_Pair1-6_P6
drwxrwxrwx 1 jhuang jhuang 4,0K Aug 15  2019  Data_Anna12_HAPDICS_HyAsP
drwxrwxrwx 1 jhuang jhuang  68K Dez 27  2019  HAPDICS_hyasp_plasmids
drwxrwxrwx 1 jhuang jhuang 8,0K Jan 14  2021  Data_Anna_HAPDICS_review
-rwxrwxrwx 1 jhuang jhuang 9,6K Jan 26  2021  data_overview.txt
drwxrwxrwx 1 jhuang jhuang 4,0K Jan 29  2021  align_assem_res_DEL
drwxrwxrwx 1 jhuang jhuang    0 Jun  8  2021 'System Volume Information'
drwxrwxrwx 1 jhuang jhuang 4,0K Jun  8  2021  EXCHANGE_DEL
drwxrwxrwx 1 jhuang jhuang 8,0K Aug 30  2021  Data_Indra_H3K4me3_public
drwxrwxrwx 1 jhuang jhuang 4,0K Feb 17  2022  Data_Gunnar_MS
drwxrwxrwx 1 jhuang jhuang 4,0K Jun  2  2022 '$RECYCLE.BIN'
drwxrwxrwx 1 jhuang jhuang 4,0K Jun  2  2022  UKE_DELLWorkstation_C_Users_indbe_Desktop
drwxrwxrwx 1 jhuang jhuang 4,0K Jun  2  2022  Linux_DELLWorkstation_C_Users_indbe_VirtualBoxVMs
drwxrwxrwx 1 jhuang jhuang 4,0K Jun 23  2022  Data_Anna_HAPDICS_RNASeq_rawdata
drwxrwxrwx 1 jhuang jhuang 8,0K Jun 23  2022  Data_Indra_H3K27ac_public
drwxrwxrwx 1 jhuang jhuang  28K Feb 22  2023  Data_Holger_Klebsiella_pneumoniae_SNP_PUBLISHING
drwxrwxrwx 1 jhuang jhuang 4,0K Dez  9  2024  DATA_INDRA_RNASEQ
drwxrwxrwx 1 jhuang jhuang 4,0K Dez  9  2024  DATA_INDRA_CHIPSEQ

jhuang@WS-2290C:/media/jhuang/Elements(jhuang_*)$ ls -ltrh
total 5,0M
-rwxr-xr-x  1 jhuang jhuang 657K Jul  9  2021 'Install Western Digital Software for Windows.exe'
-rwxr-xr-x  1 jhuang jhuang 498K Jul  9  2021 'Install Western Digital Software for Mac.dmg'
drwxr-xr-x  2 jhuang jhuang 1,0M Mai 17  2023 'System Volume Information'
drwxr-xr-x  2 jhuang jhuang 1,0M Aug 26  2024 '$RECYCLE.BIN'
drwxr-xr-x 11 jhuang jhuang 1,0M Feb  4  2025  20250203_FS10003086_95_BTR67811-0621

jhuang@WS-2290C:/media/jhuang/Smarty$ ls -tlrh
total 140K
drwx------  2 jhuang jhuang  16K Mär 14  2018 lost+found
drwxrwxrwx 21 jhuang jhuang  68K Jun 10  2022 Blast_db
drwxrwxr-x  2 jhuang jhuang 4,0K Sep  5  2022 temporary_files_DEL
drwxrwxr-x  9 jhuang jhuang  12K Sep  6  2022 ALIGN_ASSEM
drwxr-xr-x 19 jhuang jhuang 4,0K Sep 29  2022 Data_Paul_Staphylococcus_epidermidis
drwxrwxr-x 11 jhuang jhuang 4,0K Jan 26  2023 Data_16S_Degenhardt_Marius_DEL
drwxrwxr-x 16 jhuang jhuang 4,0K Jun 28  2023 Data_Gunnar_Yersiniomics_DEL
drwxrwxr-x  6 jhuang jhuang 4,0K Jul  5  2023 Data_Manja_RNAseq_Organoids_Virus
drwxrwxr-x 19 jhuang jhuang  12K Sep 27  2023 Data_Emilia_MeDIP
drwxr-xr-x 14 jhuang jhuang 4,0K Okt 30  2023 DjangoApp_Backup_2023-10-30
drwxrwxr-x  5 jhuang jhuang 4,0K Apr 19  2024 ref
drwxrwxr-x  4 jhuang jhuang 4,0K Jul 22  2025 Data_Michelle_RNAseq_2025_raw_data_DEL_AFTER_UPLOAD_GEO

Protected: SARS-CoV-2 病毒血症与免疫介导的组织侵入在 COVID-19 血管病理中的作用：一项基于尸检的研究。

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按研究方向速查：生命科学常用数据库清单（Global Core Biodata Resources 精选）

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下面是一份“按研究方向推荐常用数据库”的速查清单。按你做什么研究 → 该先去哪几个库来分组，每个库后面给一句“用来干嘛”。In summary, 做基因组先看 ENA/Ensembl/UCSC；做蛋白功能先上 UniProt/InterPro；做通路用 Reactome；做药物与小分子用 ChEMBL/ChEBI；做人类变异用 gnomAD/GWAS Catalog/ClinGen；做微生物命名和 16S 用 LPSN/SILVA；做模型生物就去 FlyBase/WormBase/ZFIN/MGD。

基因组学与序列数据

European Nucleotide Archive（ENA）：原始测序数据、组装、注释的综合归档入口（欧洲体系）。
DNA Data Bank of Japan（DDBJ）：日本序列数据归档（INSDC 成员之一）。
Ensembl：脊椎动物基因组浏览、比较基因组、变异、调控注释。
UCSC Genome Browser：人类及多物种基因组可视化浏览与注释轨道。
GENCODE：人/鼠高质量基因注释集合（常做标准参考）。

微生物/细菌方向（菌株信息、命名、16S 等）

BacDive：菌株层面的标准化信息（培养条件、表型、来源等）。
LPSN: List of Prokaryotic names with Standing in Nomenclature：原核命名权威信息（名称是否有效、分类更新）。
SILVA：16S/18S、23S/28S rRNA 序列与比对数据集（做分类/扩增子常用）。

蛋白质功能注释、家族结构域、互作网络

UniProt：蛋白序列与功能注释的“总入口”（最常用）。
InterPro：蛋白家族/结构域/功能位点整合分析（做注释和功能预测）。
CATH：蛋白结构域进化关系/结构分类。
STRING：蛋白互作网络（预测+整合证据），做功能关联很方便。
IMEx: International Molecular Exchange Consortium：高质量、人工整理的分子互作数据整合。
Protein Data Bank（PDB）：蛋白/核酸 3D 结构的全球档案库（结构生物学必备）。

通路、代谢与反应数据库

Reactome：经典通路知识库（富集分析、机制解释常用）。
Rhea：生化反应与转运反应标准化知识库（注释/代谢研究）。
BRENDA：酶功能数据大全（底物、动力学、反应等）。
EcoCyc：大肠杆菌 K-12 的基因组与代谢通路精细注释库。

化学、小分子、药物靶点（药物研发/化学生物学）

ChEBI：小分子化学实体词典/本体（标准名、结构、分类）。
ChEMBL：药物样分子、活性、靶点关联（做药物发现/重定位很常用）。
IUPHAR/BPS Guide to PHARMACOLOGY：权威药理学知识库（配体-靶点关系、药物信息）。
LIPID MAPS：脂质组学资源与命名/分类体系。

转录组、表达谱、蛋白表达图谱

Bgee：跨物种表达模式对比（“这个基因在哪里表达？”）。
GXD：小鼠基因表达数据库（发育/组织表达等）。
Human Protein Atlas：人类组织/细胞层面的蛋白表达与定位图谱。
Europe PMC：生命科学文献入口（全文/摘要、资助信息等，做调研很高效）。

人类遗传变异、GWAS、疾病本体与临床解释

gnomAD：人群变异频率汇总（过滤“常见变异”必备）。
GWAS Catalog：GWAS SNP-性状关联的标准化数据库。
Clinical Genome Resource（ClinGen）：基因/变异的临床相关性评估资源（精准医学）。
CIViC: Clinical Interpretation of Variants in Cancer：肿瘤变异临床意义的社区整理平台。
Human Disease Ontology Knowledgebase：疾病本体（统一术语、做整合分析很有用）。
ClinPGX：药物基因组学知识整理（基因变异影响用药反应）。

模型生物与专属物种数据库

FlyBase：果蝇遗传与分子数据。
WormBase：秀丽线虫及相关线虫的基因组与生物学数据。
ZFIN: The Zebrafish Information Network：斑马鱼模型数据。
MGD: Mouse Genome Database：小鼠基因组与表型/疾病关联数据。
PomBase：裂殖酵母资源库。
Saccharomyces Genome Database：出芽酵母数据库。
Rat Genome Database：大鼠基因组与表型/疾病数据。
Alliance of Genome Resources：多模型生物资源的整合入口（跨物种对照很方便）。

生物多样性、物种名录与分类学

Catalogue of Life：全球已知物种的统一名录与分类信息。
Global Biodiversity Information Facility（GBIF）：全球生物多样性观测/标本记录等开放数据平台。

病原体与媒介（寄生虫/媒介昆虫等）

VEuPathDB：真核病原体及无脊椎媒介相关的大规模组学数据库集合。

NCBI 提交入口怎么选？一张“决策树”帮你不走弯路（GenBank / SRA / Genome / TSA / BioProject / BioSample / dbGaP / GTR / ClinVar）

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很多人第一次在 NCBI 点“Start a new submission”会懵：这么多入口到底选哪个？下面给你一棵从目标出发的决策树，按着走基本不会错。如果你要公开的是“数据文件”（FASTQ/FASTA/组装/注释），不要选 GTR；如果你要公开的是“某个临床/研究检测项目的服务说明”，才选 GTR。

✅ 第一步：你要提交的是“原始测序数据”还是“组装/注释结果”？

A. 我有 FASTQ（原始 reads：Illumina/Nanopore/PacBio）

➡️ 选 Sequence Read Archive (SRA)

你提交的是：reads + 文库信息（平台、PE/SE、策略等）
几乎所有文章要求原始数据可复现，都需要 SRA

同时你通常还需要：

BioSample（每个样本的“身份证”）
BioProject（把整个项目的数据串起来）

✅ 常见路径：BioProject → BioSample → SRA

B. 我有组装好的基因组（contigs/scaffolds/complete genome）

➡️ 选 Genome（基因组提交主入口）

适合：细菌/真菌/病毒/真核的 draft 或 complete genome
会与 GenBank/Assembly 体系关联（后续可公开检索引用）

同时通常还需要：

BioSample（样本来源信息）
BioProject（项目汇总）
（可选但强烈建议）SRA（如果你也愿意公开原始 reads）

✅ 常见路径：BioProject → BioSample → SRA（可选/建议）→ Genome

C. 我只有一个基因/片段/质粒序列（不是整套基因组项目）

➡️ 选 GenBank

适合：单基因、片段序列、单独的质粒序列、特定区域序列
如果你在做“系统的基因组项目”，通常走 Genome 更合适；GenBank更像“序列条目提交”。

D. 我有转录组拼装结果（assembled transcripts，不是 reads）

➡️ 选 TSA（Transcriptome Shotgun Assembly）

TSA 提交的是：拼装后的转录本序列
原始 RNA-seq reads 仍应走 SRA

✅ 常见路径：BioProject → BioSample → SRA → TSA

✅ 第二步：你提交的是“临床敏感人类数据/变异解释/检测项目”吗？

E. 数据涉及人类受试者隐私、需要受控访问（表型+基因型/临床队列）

➡️ 选 dbGaP（受控访问）

适合：人类敏感数据
常伴随伦理/权限/审查流程（不是完全公开下载）

F. 你要提交“变异的临床意义解读”（致病性、证据、表型关联）

➡️ 选 ClinVar

适合：临床实验室/研究团队共享变异解释

G. 你要登记“遗传检测项目/检测服务信息”

➡️ 选 GTR（Genetic Testing Registry）

更像“检测项目注册”，不是上传测序数据本体

✅ 第三步：你是不是在管理一个“项目集合”？

H. 你有多个样本/多批数据/多类型数据（SRA + Genome + 其它）

➡️ 建议先建 BioProject

I. 你每一个样本都需要可追溯的元数据（来源、地点、日期、宿主等）

➡️ 基本都需要 BioSample

作用：样本身份证；SRA/Genome 通常都要挂它

终极“快速选择口诀”

FASTQ 原始 reads → SRA
基因组组装（contigs/scaffolds/complete）→ Genome
转录本拼装（transcripts）→ TSA
单基因/片段/质粒序列条目 → GenBank
把所有东西串成一个项目 → BioProject
每个样本来源信息 → BioSample
人类敏感受控数据 → dbGaP
临床变异解释 → ClinVar
遗传检测项目登记 → GTR
批量/自动化 → API

下面是对 GTR（Genetic Testing Registry，遗传检测注册库） 的更详细中文说明。

GTR 是什么？

GTR 是 NCBI 上一个“登记遗传检测项目/检测服务信息”的公共目录，由提供检测的实验室/机构自愿提交，目的是让公众、临床医生和研究人员能查到：某个疾病/基因/病原体有哪些检测、由哪些实验室提供、检测方法是什么、适用范围和证据如何等。(NCBI)

关键点：GTR 不是用来上传 FASTQ/基因组序列的。

原始测序数据 → SRA
基因组组装/注释 → Genome / GenBank
GTR → 登记“检测项目本身”的信息（类似检测项目黄页/目录） (NCBI)

GTR 收录哪些“检测”？

GTR 的范围不仅是传统“单基因遗传病检测”，也包括：

孟德尔遗传病、药物反应（药物基因组学）相关检测
肿瘤/体细胞变异检测
多基因 panel、芯片（array）、生化、细胞遗传、分子检测 (NCBI)
微生物/病原体相关检测（例如病原体 panel、病毒载量、血清学抗体/抗原检测等） (NCBI)

在 GTR 里，一个“检测条目”通常会包含哪些信息？

你可以把它理解为“一个检测项目的说明书 + 实验室信息”组合，常见字段包括：

检测目的/用途：诊断、携带者筛查、预后、用药指导等 (NCBI)
检测对象（Target）：基因/区域、变异类型、或病原体靶标等
方法学（Methodology）：例如 PCR、Sanger、NGS panel、MLPA、芯片、qPCR、Nanopore 等（写清楚平台与策略）(NCBI)
适应证/关联疾病（Indication/Condition）：对应哪些疾病/表型；并可建立“检测—靶标—适应证”的声明关系 (NCBI)
性能与证据：分析/临床有效性、参考文献、指南或标准等（GTR强调用途与证据展示）(NCBI)
实验室信息：机构名称、联系人、资质/认证信息、可提供的服务范围等 (NCBI)
GTR accession：每个检测都有唯一编号，便于在论文/EHR 中引用。(NCBI)

谁应该提交 GTR？

主要是提供遗传/分子检测服务的实验室或机构（临床检验科、第三方医学检验所、商业检测机构、研究机构实验室等）。(NCBI)

如果你只是做科研并想公开数据：

数据公开通常走 BioProject/BioSample + SRA + Genome/GenBank
不一定需要 GTR（除非你在对外提供一个“检测项目/检测服务”）(NCBI)

GTR 怎么提交？（流程概览）

GTR 提交一般是两步走：

1）先注册“实验室（Laboratory record）”

先把实验室作为一个实体登记，GTR 会审核/联系新注册者；实验室通过后才可以提交具体检测项目。(NCBI)

2）再提交“检测（Test record）”

有两种方式：

网页交互式提交：在提交门户里逐页填写信息（适合少量检测）(NCBI)
批量提交（Excel 模板）：适合大量临床检测项目；可用全字段或最小字段模板上传（研究检测的批量上传通常不开放/不支持）。(NCBI)

GTR vs ClinVar vs dbGaP：最容易混淆的三兄弟

GTR：登记“检测项目/检测服务”信息（谁提供、怎么测、测什么、适应证/证据）(NCBI)
ClinVar：提交“变异—临床意义”的解释与证据（致病性分类等）（你贴里之前也提过）
dbGaP：人类敏感数据（基因型/表型）受控访问的归档库

1) Make a single dataset folder name for GEO (recommended)

2) Prepare the GEO HTS metadata spreadsheet (REQUIRED)

STUDY tab

SAMPLES tab (most important)

PROTOCOLS tab

FILES / supplementary (if the template has it)

3) FTP upload to GEO (data files only)

4) Submit the metadata spreadsheet on the GEO web page

5) If GEO asks for raw FASTQs

1) What each platform is best for

2) Where to submit your two dataset types

3) What to choose in the NCBI “Start a new submission” list

4) Accounts / login clarification

5) Practical “Data availability” logic for a manuscript

6) ENA note (from the email context)

7) Key takeaway (one-liner)

§ 9（定居许可 / Niederlassungserlaubnis）中文翻译

§ 18（专业人才移民基本原则；一般规定）中文翻译

§9 和 §18 的核心区别（中文对比）

§18a 具备职业培训的专业人才（Fachkräfte mit Berufsausbildung）— 中文翻译

§18b 具备高等教育背景的专业人才（Fachkräfte mit akademischer Ausbildung）— 中文翻译

§18c 专业人才的定居许可（Niederlassungserlaubnis für Fachkräfte）— 中文翻译

§18d 研究（Forschung）— 中文翻译

§18g 欧盟蓝卡（Blaue Karte EU）— 中文翻译

五个条款的关键区别（中文对比）

1) Per-dataset sample inventory (compact lists)

1. Data_Tam_RNAseq_2024_AUM_MHB_Urine_on_ATCC19606

2. Data_Tam_RNAseq_2025_LB-AB_IJ_W1_Y1_WT_vs_Mac-AB_IJ_W1_Y1_WT_on_ATCC19606

3. Data_Tam_RNAseq_2025_subMIC_exposure_on_ATCC19606

4. Data_Tam_DNAseq_2023_lab_strains

5. Data_Tam_DNAseq_2025_AYE-WT_Q_S_craA-Tig4_craA-1-Cm200_craA-2-Cm200

6. Data_Tam_DNAseq_2025_E.hormaechei-adeABadeIJ_adeIJK_CM1_CM2_on_ATCC19606

7. Data_Tam_DNAseq_2025_ATCC19606-Y1Y2Y3Y4W1W2W3W4

8. Data_Tam_DNAseq_2026_19606deltaIJfluE

9. Data_Tam_DNAseq_2026_Acinetobacter_harbinensis

10. Data_Tam_Metagenomics_2026

11. Data_Foong_RNAseq_2021_ATCC19606_Cm (mapping list provided)

12. Data_Foong_DNAseq_2025_AYE_Dark_vs_Light

2) Dataset-level summary (quick lookup)

3) Complete list

/media/jhuang/INTENSO

~/DATA

~/DATA_A

~/DATA_B

~/DATA_C

~/DATA_D

~/DATA_E

~/DATA_Intenso

/media/jhuang/Titisee

/media/jhuang/Elements(Denise_ChIPseq)

/media/jhuang/Seagate Expansion Drive(HOffice)

/media/jhuang/Elements(Anna_C.arnes)

/media/jhuang/Seagate Expansion Drive(DATA_COPY_FROM_hamburg)

/media/jhuang/Seagate Expansion Drive(Seagate_1)

/media/jhuang/Seagate Expansion Drive(Seagate_2)

/media/jhuang/Elements(An14_RNAs)

/media/jhuang/Elements(Indra_HAPDICS)

/media/jhuang/Elements(jhuang_*)

/media/jhuang/Smarty

Original input (as one point)

基因组学与序列数据

微生物/细菌方向（菌株信息、命名、16S 等）

蛋白质功能注释、家族结构域、互作网络

通路、代谢与反应数据库

化学、小分子、药物靶点（药物研发/化学生物学）

转录组、表达谱、蛋白表达图谱

人类遗传变异、GWAS、疾病本体与临床解释

模型生物与专属物种数据库

生物多样性、物种名录与分类学

病原体与媒介（寄生虫/媒介昆虫等）

✅ 第一步：你要提交的是“原始测序数据”还是“组装/注释结果”？

A. 我有 FASTQ（原始 reads：Illumina/Nanopore/PacBio）

B. 我有组装好的基因组（contigs/scaffolds/complete genome）

C. 我只有一个基因/片段/质粒序列（不是整套基因组项目）

D. 我有转录组拼装结果（assembled transcripts，不是 reads）

✅ 第二步：你提交的是“临床敏感人类数据/变异解释/检测项目”吗？

E. 数据涉及人类受试者隐私、需要受控访问（表型+基因型/临床队列）

F. 你要提交“变异的临床意义解读”（致病性、证据、表型关联）

G. 你要登记“遗传检测项目/检测服务信息”

✅ 第三步：你是不是在管理一个“项目集合”？

1. `Data_Tam_RNAseq_2024_AUM_MHB_Urine_on_ATCC19606`

2. `Data_Tam_RNAseq_2025_LB-AB_IJ_W1_Y1_WT_vs_Mac-AB_IJ_W1_Y1_WT_on_ATCC19606`

3. `Data_Tam_RNAseq_2025_subMIC_exposure_on_ATCC19606`

4. `Data_Tam_DNAseq_2023_lab_strains`

5. `Data_Tam_DNAseq_2025_AYE-WT_Q_S_craA-Tig4_craA-1-Cm200_craA-2-Cm200`

6. `Data_Tam_DNAseq_2025_E.hormaechei-adeABadeIJ_adeIJK_CM1_CM2_on_ATCC19606`

7. `Data_Tam_DNAseq_2025_ATCC19606-Y1Y2Y3Y4W1W2W3W4`

8. `Data_Tam_DNAseq_2026_19606deltaIJfluE`

9. `Data_Tam_DNAseq_2026_Acinetobacter_harbinensis`

10. `Data_Tam_Metagenomics_2026`

11. `Data_Foong_RNAseq_2021_ATCC19606_Cm` (mapping list provided)

12. `Data_Foong_DNAseq_2025_AYE_Dark_vs_Light`