bio-chipseq-qc - ChIP-seq Quality Control Metrics
Calculate ChIP-seq quality control metrics including FRiP, cross-correlation, library complexity, and IDR for experiment 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
- generate fingerprint plot
- generate cross-correlation plot
- generate correlation heatmap
Inputs
- ChIP-seq BAM file
- peak file
- input BAM file
Outputs
- FRiP score
- NSC value
- RSC value
- NRF value
- PBC1 value
- PBC2 value
- IDR results
- fingerprint plot
- cross-correlation plot
- correlation heatmap
Requirements
- bedtools
- samtools
- deepTools
- phantompeakqualtools
- R
- R spp package
- pysam
- pybedtools