24398258
This reference describes dCLIP.
| PMID | PMID 24398258 |
|---|---|
| Title | dCLIP: a computational approach for comparative CLIP-seq analyses |
| Year | 2014 |
| Journal | Genome Biology |
| Author | Tao Wang, Yang Xie, Guanghua Xiao |
| Volume | 15 |
| Start page |
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Full text description
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/.
