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

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/.

SUBMITTER: Chen B

PROVIDER: S-EPMC4054095 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature

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

Chen Beibei B Yun Jonghyun J Kim Min Soo MS Mendell Joshua T JT Xie Yang Y

Genome biology 20140122 1

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 ...[more]

PMID: 24451213

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