Version Compatibility

Reference examples tested with: STAR 2.7.11+, deepTools 3.5+, 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.

MeRIP-seq Preprocessing

"Preprocess my MeRIP-seq IP and input samples" → Align and QC methylated RNA immunoprecipitation sequencing data, comparing IP enrichment to input for downstream m6A peak calling.

• CLI: STAR for splice-aware alignment, samtools for post-processing, deepTools for QC

Alignment with STAR

Goal: Align MeRIP-seq IP and input samples to the genome with splice-aware mapping for downstream peak calling.