Version Compatibility

Reference examples tested with: Bowtie2 2.5.3+, STAR 2.7.11+, samtools 1.19+

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

• 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 Alignment

"Align my CLIP-seq reads to the genome" → Map preprocessed CLIP reads with splice-aware alignment and crosslink site extraction for downstream peak calling.

• CLI: STAR with CLIP-optimized parameters (no multi-mappers, short reads)
• CLI: bowtie2 for unspliced protocols

STAR Alignment

Goal: Align CLIP-seq reads to the genome with splice awareness and strict uniqueness filtering.