articles

How to debug and construct the docker docker own_viral_ngs?

Abstract: mkdir viralngs; cd viralngs ln -s ~/Tools/viral-ngs_docker/Snakefile Snakefile ln -s ~/Tools/viral-ngs_docker/bin bin cp ~/Tools/viral-ngs_docker/refsel.acids refsel.

Variant calling for Data_Pietschmann_229ECoronavirus_Mutations_2025 (via docker own_viral_ngs)

Author: gene_x

Abstract: 1. Input data: ln -s ../raw_data_2024/hCoV229E_Rluc_R1.fastq.gz hCoV229E_Rluc_R1.fastq.gz ln -s ../raw_data_2024/hCoV229E_Rluc_R2.fastq.gz hCoV229E_Rluc_R2.fastq.gz ln -s ../r

Post-processing of DAMIAN results

Author: gene_x

Abstract: 1. Prepare input raw data # -- Ringversuch -- ~/DATA/Data_Damian/241213_VH00358_120_AAG523FM5_Ringversuch ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20579/01_RV1_DNA_S1_R

Analysis of the RNA binding protein (RBP) motifs for RNA-Seq and miRNAs (v3)

Author: gene_x

Abstract: There are several alternative R packages and tools to perform motif enrichment analysis for RNA-binding proteins (RBPs), beyond PWMEnrich::motifEnrichment(). Here are the most notable ones: | Too

Visualization and Export of miRNA Expression Profiles Using Manhattan Plots in R

Author: gene_x

Abstract: This R script processes raw miRNA read count data to visualize expression profiles across different samples using Manhattan plots. The main steps include: * Normalization: Raw counts are converted to

Analysis of the RNA binding protein (RBP) motifs for RNA-Seq and miRNAs (v2)

Author: gene_x

Abstract: There are several alternative R packages and tools to perform motif enrichment analysis for RNA-binding proteins (RBPs), beyond PWMEnrich::motifEnrichment(). Here are the most notable ones: | Too

Analysis of the RNA binding protein motifs for RNA Seq

Author: gene_x

Abstract: Analysis of the RNA binding protein motifs for RNA Seq >TODOs_NEXTWEEK: how to use RBPmap results to enrich the significant RBPs for RNA-seq (3' UTRs?) and miRNAs? 🧬 1. RBPmap (Web +

Comprehensive smallRNA-7 profiling using exceRpt pipeline with full reference databases (v3)

Author: gene_x

Abstract: 1. Input data # name condition # ---------------------------------------------- # 0403_WaGa_wt parental_cells_1.fastq.gz # #050

What type of evidence was used to assert linkage across the assembly gaps?

Author: gene_x

Abstract: * paired-ends: Paired sequences from the two ends of a DNA fragment, mate-pairs and molecular-barcoding. * align-genus: Alignment to a reference genome within the same genus. * align-xgenus:

Processing Data_Tam_RNAseq_2025_LB_vs_Mac_ATCC19606

Author: gene_x

Abstract: 1. Targets Could you please assist me with processing RNA-seq data? The reference genome is CP059040. I aim to analyze the data using PCA, a Venn diagram, and KEGG and GO annotation enrichmen