deeptools
Category: life-sciences · License: BSD license · Version: 1.3 · Includes scripts
Tags: NGS, ChIP-seq, coverage, bigWig, genomics, bioinformatics
When to use it
Runs deepTools command-line programs on NGS alignment data: bamCoverage and bamCompare for BAM to bigWig/bedGraph with RPGC, CPM, RPKM or BPM normalization, multiBamSummary with plotCorrelation and plotPCA, plotFingerprint, computeMatrix with plotHeatmap and plotProfile, and alignmentSieve with —ATACshift. Use when converting BAM files to normalized coverage tracks. Use when checking ChIP-seq quality or comparing replicates. Use when plotting signal around TSS or peak regions. Use when comparing treatment versus control samples. Use when building ChIP-seq, RNA-seq or ATAC-seq coverage workflows. Not for peak calling or differential expression analysis.Example requests
Ask your agent in plain language, for example:- “How do I turn my sorted BAM into a bigWig I can load in IGV?”
- “I have H3K27ac ChIP-seq for mouse (mm10) in treat_rep1.bam, treat_rep2.bam and input.bam, all paired-end and indexed. I need a bigWig of treatment over input as log2 ratio, and I want to check that the two replicates agree before I trust it. What commands should I run?”
- “I’ve got ATAC-seq alignments for human cells and want accessibility signal shown as a heatmap centered on transcription start sites, with the reads corrected for transposase insertion offset first. How should I do that?”
Install
/plugin marketplace add KalarisLabs/research-agent-skills and install the whole life-sciences category with /plugin install life-sciences@research-agent-skills.