Introduction

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.The software is implemented in Perl. The source code and detailed documentation are available at http://zhanglab.c2b2.columbia.edu/index.php/CTK .cz2294@columbia.edu.

Publications

  1. CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data.
    Cite this
    Shah A, Qian Y, Weyn-Vanhentenryck SM, Zhang C, 2017-02-01 - Bioinformatics (Oxford, England)
  2. Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis.
    Cite this
    Moore MJ, Zhang C, Gantman EC, Mele A, Darnell JC, Darnell RB, 2014-02-01 - Nature protocols

Credits

  1. Ankeeta Shah
    Developer

    Department of Systems BiologyDepartment of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, United States of America

  2. Yingzhi Qian
    Developer

    Department of Systems BiologyDepartment of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, United States of America

  3. Sebastien M Weyn-Vanhentenryck
    Developer

    Department of Systems BiologyDepartment of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, United States of America

  4. Chaolin Zhang
    Investigator

    Department of Systems BiologyDepartment of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, United States of America

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Summary
AccessionBT001518
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesPerl
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByChaolin Zhang