Version Compatibility

Reference examples tested with: Bowtie2 2.5.3+, STAR 2.7.11+, cutadapt 4.4+, numpy 1.26+, 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
• 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.

Ribo-seq Preprocessing

"Preprocess my ribosome profiling data" → Trim adapters, size-select ribosome-protected fragments (26-34 nt), remove rRNA contamination, and align to the transcriptome for translation analysis.

• CLI: cutadapt → bowtie2 (rRNA removal) → STAR (genome alignment)

Workflow Overview