Journal
GENOME BIOLOGY
Volume 15, Issue 1, Pages -Publisher
BMC
DOI: 10.1186/gb-2014-15-1-r11
Keywords
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Funding
- National Institutes of Health [1R01CA172211, 5R01CA152301, 4R33DA027592]
- Cancer Prevention Research Institute of Texas [RP101251]
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Although comparison of RNA-protein interaction profiles across different conditions has become increasingly important to understanding the function of RNA-binding proteins (RBPs), few computational approaches have been developed for quantitative comparison of CLIP-seq datasets. Here, we present an easy-to-use command line tool, dCLIP, for quantitative CLIP-seq comparative analysis. The two-stage method implemented in dCLIP, including a modified MA normalization method and a hidden Markov model, is shown to be able to effectively identify differential binding regions of RBPs in four CLIP-seq datasets, generated by HITS-CLIP, iCLIP and PAR-CLIP protocols. dCLIP is freely available at http://qbrc.swmed.edu/software/.
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