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Tools
Tools
| Item Type: | Article |
|---|---|
| Title: | A pipeline for PAR-CLIP data analysis |
| Creators Name: | Jens, M. |
| Abstract: | Photo-activatable ribonucleoside cross-linking and immunoprecipitation (PAR-CLIP) is a method to detect binding sites of RNA-binding proteins (RBPs) transcriptome-wide. This chapter covers the computational analysis of the high-throughput sequencing reads generated from PAR-CLIP experiments. It explains how the reads are mutated due to UV cross-linking and how to appropriately pre-process and align them to a reference sequence. Aligned reads are then aggregated into clusters which represent putative RBP-binding sites. Mapping artifacts are a source of false positives, which can be controlled by means of a mapping decoy and adaptive quality filtering of the read clusters. A step-by-step explanation of this procedure is given. All necessary tools are open source, including the scripts presented and used in this chapter. |
| Keywords: | PAR-CLIP, CLIP, UV, Cross-Linking, Next-Generation Ssequencing, High-Throughput, Transcriptome, RNA, Small RNA, miRNA, mRNA, RNA-Binding Protein, RBP, Binding Site, FLEXBAR, Adapter Removal, Read Mapping, BWA, False-Positive Filtering, BWA PSSM, Consensus-Binding Sites |
| Source: | Methods in Molecular Biology |
| Series Name: | Methods in Molecular Biology |
| Title of Book: | Post-Transcriptional Gene Regulation |
| ISSN: | 1064-3745 |
| ISBN: | 978-1-4939-3066-1 |
| Publisher: | Springer / Humana Press |
| Volume: | 1358 |
| Page Range: | 197-207 |
| Number of Pages: | 353 |
| Date: | 2016 |
| Official Publication: | https://doi.org/10.1007/978-1-4939-3067-8_12 |
| PubMed: | View item in PubMed |
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