期刊
GENOME BIOLOGY
卷 15, 期 1, 页码 -出版社
BMC
DOI: 10.1186/gb-2014-15-1-r18
关键词
-
资金
- NIH [5R01CA152301, 4R33DA027592]
- NASA [NNJ05HD36G, CPRIT R1008, NIH R01CA120185, P01CA134292, CPRIT RP101251]
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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