PIPE-CLIP: A comprehensive online tool for CLIP-seq data analysis

Beibei Chen, Jonghyun Yun, Min Soo Kim, Joshua T. Mendell, Yang Xie

Research output: Contribution to journalArticlepeer-review

66 Scopus citations


CLIP-seq is widely used to study genome-wide interactions between RNA-binding proteins and RNAs. However, there are few tools available to analyze CLIP-seq data, thus creating a bottleneck to the implementation of this methodology. Here, we present PIPE-CLIP, a Galaxy framework-based comprehensive online pipeline for reliable analysis of data generated by three types of CLIP-seq protocol: HITS-CLIP, PAR-CLIP and iCLIP. PIPE-CLIP provides both data processing and statistical analysis to determine candidate cross-linking regions, which are comparable to those regions identified from the original studies or using existing computational tools.

Original languageEnglish (US)
Article numberR18
JournalGenome biology
Issue number1
StatePublished - 2014

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology


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