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Genome Biol. 2014 Jan 7;15(1):R11. doi: 10.1186/gb-2014-15-1-r11.

dCLIP: a computational approach for comparative CLIP-seq analyses.

Abstract

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/.

PMID:
24398258
[PubMed - in process]
PMCID:
PMC4054096
Free PMC Article

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