atac-footprinting

npx skills add majiayu000/claude-skill-registry --skill 28-atacseq-footprint --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

# ATAC-seq Footprint Analysis using TOBIAS ## 1. Overview This skill performs TF footprint detection and optional differential TF binding analysis using TOBIAS. It identifies true TF occupancy by modeling depletion of Tn5 insertions at motif cores. Main steps include: - Refer to the **Inputs & Outputs** section to check required inputs and set up the output directory structure. - **Always prompt user** for genome assembly used. - **Always prompt user** if other required files are missing. - Tn5 bias correction with ATACorrect. - Motif scanning. - Footprint scoring. - Binding detection with BINDetect. - Aggregate footprint visualization. --- ## 2. When to use this skill Use this skill when you need to identify transcription factor occupancy using ATAC-seq data. It is suitable for: - Mapping TF binding events without ChIP-seq. - Comparing TF footprint strength between conditions or cell types. - Identifying which TFs gain or lose binding activity during differentiation or perturbation. - Supporting integrative regulatory analyses with RNA-seq, ChIP-seq, or chromatin conformation data. Recommended data requirements: - Biological replicates are preferred (≥2 per condition). - ≥30M pair

ATAC_footprint_analysis/
motifs.bed                  # motif genomic coordinates
scan.log
score.log
motif_activity.txt          # differential TF activity (if applicable)
bindetect.log
aggregate.log
logs/ # all logs
temp/ # intermediate files