bio-chipseq-qc - ChIP-seq Quality Control
Calculate FRiP, NSC/RSC, library complexity, and IDR metrics for ChIP-seq quality assessment
Tags
Updated: 2026-05-28Capabilities
Typical Inputs
Typical Outputs
What this skill does
- calculate FRiP
- calculate NSC
- calculate RSC
- calculate NRF
- calculate PBC1
- calculate PBC2
- run IDR analysis
- compare biological replicates
- generate fingerprint plots
- compute TSS enrichment
- plot sample correlation
- generate QC report
Inputs
- ChIP-seq BAM file
- peak file
- input control BAM file
- replicate BAM files
Outputs
- FRiP score
- NSC value
- RSC value
- NRF score
- PBC1 score
- PBC2 score
- IDR results
- fingerprint plot
- correlation heatmap
- QC report
Requirements
- deepTools
- phantompeakqualtools
- IDR
- bedtools
- samtools
- macs3
- Python with pysam
- R with spp