Version Compatibility

Reference examples tested with: MACS3 3.0+, Subread 2.0+, bedtools 2.31+, deepTools 3.5+, pybedtools 0.9+, pysam 0.22+, samtools 1.19+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• R: packageVersion('<pkg>') then ?function_name to verify parameters
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

ChIP-seq Quality Control

"Assess the quality of my ChIP-seq experiment" → Compute FRiP, cross-correlation (NSC/RSC), library complexity, and IDR replicate concordance to evaluate enrichment success.

• CLI: deeptools plotFingerprint, phantompeakqualtools run_spp.R
• Python: pysam + pybedtools for custom QC metrics

Quality metrics for assessing ChIP-seq experiment success and replicate reproducibility.

FRiP (Fraction of Reads in Peaks)

Goal: Quantify enrichment strength by measuring the proportion of reads falling within called peaks.

Approach: Count reads overlapping peak regions and divide by total mapped reads.

Calculate FRiP with bedtools

# Count reads in peaks
reads_in_peaks=$(bedtools intersect -a chip.bam -b peaks.narrowPeak -u | samtools view -c -)
total_reads=$(samtools view -c -F 260 chip.bam)

# Calculate FRiP
frip=$(echo "scale=4; $reads_in_peaks / $total_reads" | bc)
echo "FRiP: $frip"

Calculate FRiP with featureCounts

# Convert peaks to SAF format
awk 'BEGIN{OFS="\t"} {print $4, $1, $2, $3, "."}' peaks.narrowPeak > peaks.saf

# Count reads in peaks
featureCounts -a peaks.saf -F SAF -o peak_counts.txt chip.bam

# FRiP from summary
grep -v "^#" peak_counts.txt.summary

Calculate FRiP with pysam

import pysam
import pybedtools