domains / families / science / clip-alignment

clip-alignment

separate

Align preprocessed CLIP-seq reads (eCLIP, iCLIP, iCLIP2, PAR-CLIP) to genome with STAR or bowtie2 using crosslink-preserving parameters, choosing between unique-mapper-only and multi-mapper-aware alignment for repeat-binding RBPs, deciding STAR vs HISAT2 memory trade-offs, and applying ENCODE-compatible filters. Use when turning preprocessed CLIP FASTQ into a deduplicated, MAPQ-filtered BAM ready for peak calling or crosslink-site detection.

When to use

• Aligning preprocessed CLIP-seq reads
• eCLIP, iCLIP, iCLIP2, PAR-CLIP alignment
• Unique-mapper-only alignment
• Multi-mapper-aware alignment for repeat-binding RBPs
• STAR vs HISAT2 memory trade-offs
• Applying ENCODE-compatible filters
• Producing deduplicated, MAPQ-filtered BAM

When not to use

• Transcriptome alignment
• Pseudo-alignment
• ATAC/ChIP alignment
• DNA alignment without splice support

Skill page

Source