CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data

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UV cross-linking and immunoprecipitation (CLIP), followed by high-throughput sequencing, is a powerful biochemical assay that maps in vivo protein-RNA interactions on a genome-wide scale. The CLIP Tool Kit (CTK) aims at providing a set of tools for flexible, streamlined and comprehensive CLIP data analysis. This software package extends the scope of our original CIMS package.

Availability and Implementation:

The software is implemented in Perl. The source code and detailed documentation are available at


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