CTK (CLIP Tool Kit)

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Description

Crosslinking and immunoprecipitation paired with highthroughput sequencing (HITS-CLIP or CLIP-Seq) has now been widely used to map protein-RNA interactions on a genome-wide scale. The CLIP Tool Kit (CTK) 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 expansion of our previous CIMS package.

Availability

CTK (CLIP Tool Kit) is available in these versions:

  • 1.0.7 (released January 2017)
  • 1.0.8

Use

 # First, load the modulefile to prepare the environment
 module add ctk-1.0.8

 # Now you can run the CTK scripts, for example:
 fastq_filter.pl --help

Documentation

https://zhanglab.c2b2.columbia.edu/index.php/CTK_Documentation

Licence

GNU General Public License (version 3

Program manager

meta@cesnet.cz

Homepage

https://zhanglab.c2b2.columbia.edu/index.php/CTK_Documentation