bio-workflows-clip-pipeline

End-to-end CLIP-seq analysis from FASTQ files to motif enrichment is orchestrated by automating UMI extraction, adapter trimming, alignment, deduplication, peak calling, and annotation. The workflow provides explicit steps and quality checkpoints to produce robust binding site and motif results.

Yes, this CLIP-seq pipeline supports eCLIP and PAR-CLIP workflows, alongside HITS-CLIP and iCLIP. It handles the specific preprocessing, peak calling, and binding-site annotation requirements for these multiple CLIP variants to identify protein-RNA interactions.

CLIP-seq preprocessing and peak calling require standard bioinformatics tools including UMI-tools, STAR, samtools, bedtools, clipper, and HOMER. The pipeline orchestrates these dependencies to execute UMI extraction, alignment, deduplication, and motif analysis.

UMI extraction and deduplication in iCLIP data analysis function by extracting unique molecular identifiers before alignment and removing PCR duplicates afterward. The pipeline leverages UMI-tools to perform these steps, ensuring accurate quantification of RNA-binding protein sites.

The best way to identify RNA-binding protein motifs from CLIP-seq peaks is through motif enrichment analysis on the identified binding sites. The pipeline applies HOMER to discover enriched sequences after peak calling and annotation are completed.

Yes, STAR alignment output can be used for CLIP-seq peak calling and annotation after deduplication. The workflow processes aligned reads through samtools and bedtools, passing them to clipper for peak calling and subsequent binding-site annotation.