Version Compatibility

Reference examples tested with: deepTools 3.5+, Picard 3.1+, samtools 1.19+, bedtools 2.31+, ATACseqQC 1.26+, pysam 0.22+, pyBigWig 0.3+, numpy 1.26+, pandas 2.2+, MultiQC 1.21+.

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.

ATAC-seq Quality Control

"Does my ATAC library pass ENCODE quality criteria?" -> Compute the seven canonical metrics (depth, alignment rate, mitochondrial fraction, library complexity, fragment-size periodicity, TSS enrichment, FRiP) and compare against ENCODE 4 thresholds, then diagnose failures.

• CLI: picard CollectInsertSizeMetrics, samtools flagstat, samtools idxstats
• CLI: deeptools plotFingerprint, computeMatrix reference-point + plotProfile
• R: ATACseqQC::TSSEscore, ATACseqQC::fragSizeDist, ATACseqQC::PTscore
• Python: custom NRF/PBC from coordinate hash; pyBigWig for TSS enrichment