Version Compatibility

Reference examples tested with: cutadapt 4.4+, fastp 0.23+, matplotlib 3.8+

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.

Small RNA Preprocessing

"Preprocess my small RNA-seq reads" → Remove 3' adapter sequences and size-select reads in the small RNA range (18-30 nt for miRNA, 24-32 nt for piRNA) before quantification or discovery.

• CLI: cutadapt -a ADAPTER -m 18 -M 30 -o trimmed.fastq input.fastq

Adapter Trimming with Cutadapt

Goal: Remove 3' adapter sequences and size-select reads in the small RNA range.