CTK (the CLIP Tool Kit) is a software package that provides a set of tools for analysis of CLIP data starting from the raw reads generated by the sequencer. It includes pipelines to filter and map reads, collapse PCR duplicates to obtain unique CLIP tags, define CLIP tag clusters and call peaks, and define the exact protein-RNA crosslink sites by CIMS and CITS analysis. This software package is an expanded version of our previous CIMS package.
- Linux / MacOsX / Windows
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CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data.
Shah A, Qian Y, Weyn-Vanhentenryck SM, Zhang C.
Bioinformatics. 2017 Feb 15;33(4):566-567. doi: 10.1093/bioinformatics/btw653.
Nat Biotechnol. 2011 Jun 1;29(7):607-14. doi: 10.1038/nbt.1873.
Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data.
Zhang C, Darnell RB.