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Updated: Mar 12, 2026

3' End Sequencing Library Preparation with A-seq2
Published on: October 10, 2017
CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data
Ankeeta Shah1, Yingzhi Qian1, Sebastien M Weyn-Vanhentenryck1
1Department of Systems BiologyDepartment of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA.
Summary:
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 http://zhanglab.c2b2.columbia.edu/index.php/CTK .
Contact:
cz2294@columbia.edu.

