Version Compatibility

Reference examples tested with: cutadapt 4.4+, pysam 0.22+

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 Preprocessing

"Preprocess my CLIP-seq reads" → Extract UMIs, trim adapters, and remove PCR duplicates from raw CLIP/iCLIP/eCLIP reads to prepare for alignment and peak calling.

• CLI: umi_tools extract for UMI handling, cutadapt for adapter trimming

UMI Extraction (eCLIP/iCLIP)

Goal: Extract UMI barcodes from CLIP-seq reads and append them to read names for downstream deduplication.