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

Beibei Chen1, Jonghyun Yun1, Min Soo Kim12, Joshua T Mendell23 and Yang Xie12*

Author Affiliations

1 Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Suite NC8.512 6000 Harry Hines Blvd, Dallas, TX 75390, USA

2 Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Suite Nc8.512 6000 Harry Hines Blvd, Dallas, TX 75390, USA

3 Department of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA

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Genome Biology 2014, 15:R18  doi:10.1186/gb-2014-15-1-r18

Published: 22 January 2014

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/ webcite.