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

Ankeeta Shah; Yingzhi Qian; Sebastien M Weyn-Vanhentenryck; Chaolin Zhang

doi:10.1093/bioinformatics/btw653

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

Bioinformatics. 2017 Feb 15;33(4):566-567. doi: 10.1093/bioinformatics/btw653.

Authors

Ankeeta Shah¹, Yingzhi Qian¹, Sebastien M Weyn-Vanhentenryck¹, Chaolin Zhang¹

Affiliation

¹ Department of Systems BiologyDepartment of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA.

Abstract

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: [email protected].

MeSH terms

High-Throughput Nucleotide Sequencing / methods*
Humans
Immunoprecipitation / methods*
Protein Binding
RNA / metabolism*
RNA-Binding Proteins / metabolism*
Sequence Analysis, RNA / methods
Software*

Substances

RNA-Binding Proteins
RNA

Abstract

MeSH terms

Substances

Grants and funding