Version Compatibility

Reference examples tested with: bedtools 2.31+, deepTools 3.5+, numpy 1.26+, pandas 2.2+, picard 3.1+, pyBigWig 0.3+, 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.

ATAC-seq Quality Control

"Check the quality of my ATAC-seq library" → Evaluate fragment size distribution (nucleosome periodicity), TSS enrichment, FRiP, and library complexity to assess chromatin accessibility experiment quality.

• CLI: deeptools bamPEFragmentSize, picard CollectInsertSizeMetrics
• Python: pysam for custom fragment analysis

Fragment Size Distribution