PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis.
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/.
Beibei
B
Chen
Jonghyun
J
Yun
Min Soo
MS
Kim
Joshua T
JT
Mendell
Yang
Y
Xie
D000818:Animals; D001665:Binding Sites / Q000235:genetics; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D047468:Immunoprecipitation / Q000379:methods*; D051379:Mice; D012313:RNA / Q000235:genetics / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
D016601:RNA-Binding Proteins; D012313:RNA