Introduction

Immunoprecipitation of RNA binding proteins (RBPs) after in vivo crosslinking, coupled with sequencing of associated RNA footprints (HITS-CLIP, CLIP-seq), is a method of choice for the identification of RNA targets and binding sites for RBPs. Compared with RNA-seq, CLIP-seq analysis is widely diverse and depending on the RBPs that are analyzed, the approaches vary significantly, necessitating the development of flexible and efficient informatics tools. In this study, we present CLIPSeqTools, a novel, highly flexible computational suite that can perform analysis from raw sequencing data with minimal user input. It contains a wide array of tools to provide an in-depth view of CLIP-seq data sets. It supports extensive customization and promotes improvization, a critical virtue, since CLIP-seq analysis is rarely well defined a priori. To highlight CLIPSeqTools capabilities, we used the suite to analyze Ago-miRNA HITS-CLIP data sets that we prepared from human brains.

Publications

  1. CLIPSeqTools--a novel bioinformatics CLIP-seq analysis suite.
    Cite this
    Maragkakis M, Alexiou P, Nakaya T, Mourelatos Z, 2016-01-01 - RNA (New York, N.Y.)

Credits

  1. Manolis Maragkakis
    Developer

    Department of Pathology and Laboratory Medicine, Division of Neuropathology, United States of America

  2. Panagiotis Alexiou
    Developer

    Department of Pathology and Laboratory Medicine, Division of Neuropathology, United States of America

  3. Tadashi Nakaya
    Developer

    Laboratory of Neuroscience, Graduate School of Pharmaceutical Sciences, Japan

  4. Zissimos Mourelatos
    Investigator

    Department of Pathology and Laboratory Medicine, Division of Neuropathology, United States of America

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Summary
AccessionBT000874
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesPerl
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByZissimos Mourelatos