Version Compatibility

Reference examples tested with: MACS3 3.0+, bedtools 2.31+, pandas 2.2+, 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
• 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.

CLIP-seq Peak Calling

"Call binding sites from my CLIP-seq data" → Identify protein-RNA interaction sites from aligned CLIP reads using specialized peak callers that model crosslink-induced signatures.

• CLI: clipper -b aligned.bam -s hg38 -o peaks.bed (CLIPper)
• CLI: pureclip -i aligned.bam -bai aligned.bam.bai -g genome.fa -o sites.bed (PureCLIP)

CLIPper (Recommended)