CTK (CLIP Tool Kit)

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.

License

GNU General Public License (version 3

Usage

Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of ctk and load default version of ctk as

module avail ctk/ # list available modules
module load ctk   # load (default) module

If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail ctk

and choose explicit version you want to use.

Documentation

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

Homepage

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