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

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

(Profiled Authors: Joshua T Mendell; Yang Xie)

Genome Biology. 2014:R18.

Abstract

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. PIPE-CLIP is available at http://pipeclip.qbrc.org/.

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