Version history

Initial release of nf-core/clipseq, created with the nf-core template.

Pipeline summary

  1. Adapter and quality trimming (Cutadapt)
  2. Pre-mapping to e.g. rRNA and tRNA sequences (Bowtie 2)
  3. Genome mapping (STAR)
  4. UMI-based deduplication (UMI-tools)
  5. Crosslink identification (BEDTools)
  6. Bedgraph coverage track generation (BEDTools)
  7. Peak calling (multiple options):
    • iCount
    • Paraclu
    • PureCLIP
    • Piranha
  8. Motif detection (DREME)
  9. Quality control:
    • Sequencing quality control (FastQC)
    • Library complexity (Preseq)
    • Regional distribution (RSeQC)
  10. Overall pipeline run and QC summaries and peak calling comparisons (MultiQC)