Analysis of ChIP-Seq and RNA-Seq Data with BioWardrobe

  • Sushmitha Vallabh
  • Andrey V. Kartashov
  • Artem Barski
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1783)

Abstract

The massive amount of information produced by ChIP-Seq, RNA-Seq, and other next-generation sequencing-based methods requires computational data analysis. However, biologists performing these experiments often lack training in bioinformatics. BioWardrobe aims to bridge this gap by providing a convenient user interface and by automating routine data-processing steps. This protocol details the use of BioWardrobe for identifying and visualizing ChIP-Seq peaks, calculating RPKMs, performing differential binding or gene expression analysis, and creating plots and heat maps. We specifically describe how to use BioWardrobe’s quality control measures for troubleshooting NGS-based experiments.

Key words

Next-generation sequencing ChIP-Seq RNA-Seq ATAC-Seq DNase-Seq RPKM Peak calling Heatmaps Epigenomics Transcriptomics 

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Sushmitha Vallabh
    • 1
  • Andrey V. Kartashov
    • 1
  • Artem Barski
    • 1
    • 2
    • 3
  1. 1.Division of Allergy and ImmunologyCincinnati Children’s Hospital Medical CenterCincinnatiUSA
  2. 2.Division of Human Genetics Cincinnati Children’s Hospital Medical CenterCincinnatiUSA
  3. 3.Department of PediatricsUniversity of Cincinnati College of MedicineCincinnatiUSA

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