Convert BAM alignments into normalized bigWig coverage tracks and generate QC plots.
npx skills add https://github.com/shushuzn/Rairos --skill deeptools-shushuzn
Please help me install this Agent Skill. Skill: deeptools Source: https://github.com/shushuzn/Rairos/tree/main/skills/deeptools Command: npx skills add https://github.com/shushuzn/Rairos --skill deeptools-shushuzn
deepTools helps you convert high-throughput sequencing alignments into normalized coverage tracks, run core quality-control checks, and generate heatmaps/profiles that reveal biological signal quality and sample similarity.
Use the attached command request: "Generate an end-to-end ChIP-seq QC workflow for my indexed BAM files and output the correlation, PCA, coverage, and fingerprint plots."
High-intent search queries and answers about installing and using this skill.
To convert BAM to bigWig for ChIP-seq and ATAC-seq, you generate normalized coverage tracks using RPGC or CPM methods. This produces bigWig or bedGraph files suitable for genome browser visualization and downstream heatmap plotting.
Generating publication-style heatmaps and metaprofiles involves creating TSS-centered or peak-centered matrices from normalized coverage tracks. You then render these matrices into visual heatmaps and metaprofiles to assess biological signal quality for ChIP-seq, RNA-seq, and ATAC-seq.
Running NGS QC and replicate comparison for ChIP-seq involves computing correlation, PCA, and coverage diagnostics. You also generate fingerprint plots and fragment-size validation to assess replicate similarity and validate ChIP enrichment before deeper interpretation.
Yes, you can create strand-specific coverage tracks for RNA-seq from indexed BAM files. The process converts alignments into normalized bigWig tracks while applying RNA-seq specific handling to maintain strand information for accurate genome browser visualization.
The workflow supports ATAC-seq analysis by applying Tn5 correction during coverage generation and feature-centered visualization. It also generates log2 enrichment tracks to compare treatment versus control samples for ATAC-seq and ChIP-seq experiments.
Yes, indexed BAM files are required to generate ready-to-run bash templates for NGS workflows. The deterministic execution relies on indexed sequencing alignments to produce QC plots, coverage tracks, and heatmaps for ChIP-seq, RNA-seq, and ATAC-seq experiment types.
zongtingweiAutomate read alignment workflows to produce sorted, indexed BAM/CRAM files with mapping metrics.
TianGzlabPerform ATAC-seq and ChIP-seq peak calling with MACS3 and motif enrichment using Homer.
LeonChaoXConvert BAM alignment files into normalized genome coverage tracks and perform QC.
ovachieverConvert BAM alignments into normalized coverage tracks and generate QC metrics.
