• Requirements
• Installation
• Basic Usage
• Usage
  • Pre-processing
  • Alignment
  • Peak calling
  • Motif discovery
• Frequently asked questions
• Copyright and License
• Tutorial

This documentation is for CLIPipe version: 1.0.3

CLIPipe is an integrated pipeline for analyzing CLIP sequencing data. It provides all the commands needed to process CLIP-seq data, and it could identify sites of protein-RNA interactions on RNA from CLIP-seq data.

CLIPipe's input is the raw FASTQ file of CLIP-seq, and its main output is BED files with identified cross-linked sites.

Several other analyses are also included in CLIPipe that provide insights into the properties of protein-RNA interaction.

The CLIPipe workflow consists of:

• Pre-processing function:
  • Quality control, adapter removal, low-quality reads filtering, duplicates collapsing, and barcode removal of the raw CLIP-seq data.
• Alignment function:
  • Mapping pre-processed data to reference genome using bowtie, bwa, and novoalign
• Peak calling function:
  • Binding peak enrichment using Piranha, CTK, PureCLIP, iCLIPro, iCount, JAMM, PeakRanger, and clipcontext
• Motif discovery function:
  • Motif discovery of the binding regions using HOMER, PhyloGibbs, MEME, GraphProt, DREME and STREME