Convert BAM alignments into normalized coverage tracks and generate QC metrics.
npx skills add https://github.com/ovachiever/droid-tings --skill deeptools
Please help me install this Agent Skill. Skill: deeptools Source: https://github.com/ovachiever/droid-tings/tree/main/skills/deeptools Command: npx skills add https://github.com/ovachiever/droid-tings --skill deeptools
deepTools is an NGS data analysis toolkit that streamlines QC, normalization, and visualization for ChIP-seq, RNA-seq, ATAC-seq, and more.
Install deeptools and use the included workflows to generate QC reports and coverage plots from BAM/BigWig files.
High-intent search queries and answers about installing and using this skill.
BAM to coverage track conversion uses bamCoverage to transform BAM alignments into bigWig or bedGraph formats with normalization methods like RPKM, CPM, BPM, RPGC, or SES, enabling standardized comparison across samples and genome sizes.
Sample comparison uses bamCompare to generate normalized difference tracks between BAM files, then plotProfile or plotHeatmap visualize enrichment patterns, fold-changes, and region-centric contrasts for publication-ready figures.
QC assessment uses plotFingerprint to evaluate library complexity and fragment distribution, along with file validation workflows that flag alignment issues, duplication rates, and coverage anomalies before downstream analysis.
Matrix computation via computeMatrix organizes coverage data across genomic regions, then plotHeatmap and plotProfile render sorted, scaled visualizations with multiple normalization and binning options for heatmaps and aggregate profiles.
Yes, deepTools supports ChIP-seq, RNA-seq, ATAC-seq, MNase-seq, and related workflows by accepting BAM and bigWig inputs with configurable effective genome sizes and normalization methods across all protocol types.
Required inputs are BAM or bigWig files and an effective genome size parameter (--effectiveGenomeSize) specific to your organism; BED files define analysis regions for matrix computation and visualization.
jasrajtulsiValidates input files and generates templates for deepTools workflows.
MDheweiAnnotate ATAC-seq or ChIP-seq peaks with genomic context and QC metrics.
hxk622Convert BAM files to bigWig and generate genomic heatmaps.
jimmc414Convert BAM files to normalized bigWig coverage tracks.
