Author: gene_x

Abstract: 1. TODO on sage check the alignment of the reads to the annotation which sent from Munich is very bad, using the reference X14112 instead, find the CMV-GFP in the genome. Using alignment to detec

Author: gene_x

Abstract: [](/static/chrHsv1_genomic_annotation/chrHsv1_s17

Author: gene_x

Abstract: 1. Verwenden Sie Mamba: Mamba ist eine schnellere Alternative zu Conda und kann Pakete und deren Abhängigkeiten schneller auflösen und installieren. Sie können es mit 'conda install mamba' installiere

Author: gene_x

Abstract: A common tool to utilize RNAseq data to correct or enhance a reference genome, especially for viruses, is StringTie. This tool is primarily designed for transcript assembly and quantification based on

Author: gene_x

Abstract: 1. Herpes Simplex Virus 1 (HSV-1) and Herpes Simplex Virus 2 (HSV-2) are closely related viruses that belong to the Herpesviridae family. Both viruses have a similar genomic structure but differ in th

Author: gene_x

Abstract: 0. nextflow (rnaseq) [jhuang@sage Data_Denise_LT_RNAseq]$ nextflow run rnaseq/main.nf --input samplesheet.csv --outdir results_GRCh38 --genome GRCh38 -profile test_full -resume --max_memor

Author: gene_x

Abstract: Volcano plots are graphical representations of the significance versus fold-change for values obtained from a particular data analysis. They are especially useful in high-throughput studies, such as g

Author: gene_x

Abstract: 1. a dashed vertical line dividing two sets of rectangular bars. [](/static/reproducing_plots_in_Methods/plot1.png "plot1.png"

Author: gene_x

Abstract: 1. Merge re-sequenced FastQ files (cat) 2. Sub-sample FastQ files and auto-infer strandedness (fq, Salmon) 3. Read QC (FastQC) 4. UMI extraction (UMI-tools) 5. Adapter and quality trimming (Trim Galor

Author: gene_x

Abstract: #nextflow run rnaseq --reads '/home/jhuang/DATA/Data_Denise_tx_epi_MCPyV/Raw_Data_RNAseq_K331A/*.fastq.gz' --fasta /home/jhuang/REFs/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa --gt