title: CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data.
abstract: 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.
authors: Department of Systems BiologyDepartment of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA.
authors: Ankeeta
authors: A
authors: Shah
authors: Department of Systems BiologyDepartment of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA.
authors: Yingzhi
authors: Y
authors: Qian
authors: Department of Systems BiologyDepartment of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA.
authors: Sebastien M
authors: SM
authors: Weyn-Vanhentenryck
authors: Department of Systems BiologyDepartment of Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA.
authors: Chaolin
authors: C
authors: Zhang
mesh_terms: D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D047468:Immunoprecipitation / Q000379:methods*; D011485:Protein Binding; D012313:RNA / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000378:metabolism*; D017423:Sequence Analysis, RNA / Q000379:methods; D012984:Software
chemical_list: D016601:RNA-Binding Proteins; D012313:RNA