Difference between revisions of "DCLIP"
m (Text replace - "Alignment Analysis" to "Sequence alignment analysis") |
|||
Line 2: | Line 2: | ||
|sw summary=dCLIP is a Perl program for discovering differential binding regions in two comparative CLIP-Seq (HITS-CLIP, PAR-CLIP or iCLIP) experiments. | |sw summary=dCLIP is a Perl program for discovering differential binding regions in two comparative CLIP-Seq (HITS-CLIP, PAR-CLIP or iCLIP) experiments. | ||
|bio domain=CLIP-Seq, HITS-CLIP, PAR-CLIP, iCLIP | |bio domain=CLIP-Seq, HITS-CLIP, PAR-CLIP, iCLIP | ||
− | |bio method= | + | |bio method=Sequence alignment analysis, |
|bio tech=NGS | |bio tech=NGS | ||
|created by=Tao Wang | |created by=Tao Wang |
Latest revision as of 12:44, 3 November 2015
Application data |
|
Created by | Tao Wang |
---|---|
Biological application domain(s) | CLIP-Seq, HITS-CLIP, PAR-CLIP, iCLIP |
Principal bioinformatics method(s) | Sequence alignment analysis |
Technology | NGS |
Created at | UT Southwestern Medical Center |
Maintained? | Yes |
Input format(s) | SAM |
Output format(s) | BED, BEDGRAPH, .txt |
Programming language(s) | Perl, C |
Software libraries | PDL, PDL::Stats |
Operating system(s) | UNIX, Unix-like |
Contact: | tao.wang@utsouthwestern.edu |
Summary: dCLIP is a Perl program for discovering differential binding regions in two comparative CLIP-Seq (HITS-CLIP, PAR-CLIP or iCLIP) experiments.
"Error: no local variable "counter" was set." is not a number.
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/.
Links
References
To add a reference for DCLIP, enter the PubMed ID in the field below and click 'Add'.
Search for "DCLIP" in the SEQanswers forum / BioStar or:
Web Search | Wiki Sites | Scientific |
---|---|---|