PIPE-CLIP：用于CLIP-seq数据分析的综合在线工具。

Chen Beibei, Yun Jonghyun, Kim Min Soo, Mendell Joshua T, Xie Yang

Genome Biol. 2014 Jan 22;15(1):R18. doi: 10.1186/gb-2014-15-1-r18.

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/.

CLIP-seq被广泛用于研究全基因组范围内RNA结合蛋白与RNA之间的相互作用。然而，用于分析CLIP-seq数据的工具很少，因此成为该方法实施的一个瓶颈。在此，我们展示了PIPE-CLIP，这是一个基于Galaxy框架的综合性在线流程，用于可靠分析由三种CLIP-seq协议（HITS-CLIP、PAR-CLIP和iCLIP）生成的数据。PIPE-CLIP提供数据处理和统计分析，以确定候选交联区域，这些区域与从原始研究或使用现有计算工具识别出的区域具有可比性。可通过http://pipeclip.qbrc.org/访问PIPE-CLIP。