Version Compatibility

Reference examples tested with: FastQC 0.12+, STAR 2.7.11+, bedtools 2.31+, cutadapt 4.4+, 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 Pipeline

"Analyze my CLIP-seq data from FASTQ to binding sites and motifs" → Orchestrate UMI extraction, adapter trimming, STAR alignment, PCR deduplication, CLIPper/PureCLIP peak calling, binding site annotation, and HOMER motif enrichment.

Pipeline Overview

FASTQ → QC → UMI extract → Trim adapters → Align → Filter → Dedup → Peak call → Annotate → Motifs