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clip-preprocessing

separate

Preprocess CLIP-seq reads (eCLIP, iCLIP, iCLIP2, iCLIP3, irCLIP, PAR-CLIP, FLASH) with protocol-specific UMI extraction, adapter trimming, length filtering, and post-alignment PCR-duplicate collapse. Use when raw CLIP FASTQ must be turned into deduplicated, crosslink-preserving BAM input for peak calling; choosing between two-pass and single-pass adapter trimming; deciding minimum read length; or mapping UMI patterns to specific eCLIP/iCLIP/iCLIP2/iCLIP3 library preps.

When to use

• UMI extraction
• adapter trimming
• length filtering
• post-alignment PCR-duplicate collapse
• choosing between two-pass and single-pass adapter trimming
• deciding minimum read length
• mapping UMI patterns to specific eCLIP/iCLIP/iCLIP2/iCLIP3 library preps

When not to use

• peak calling

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