Project

General

Profile

BioWardrobe

Experiment Management System

Introduction

BioWardrobe is a software package for storing and analyzing ChIP-Seq, RNA-Seq and similar datasets. The Wardrobe workflow is separated into two parts, preliminary analysis and advanced analysis. During preliminary analysis, sequence data are downloaded, processed, evaluated for quality and mapped onto a local mirror of the genome browser. Advanced analysis involves comparing and integrating different datasets.

Access

Wardrobe source code and installation guide can be downloaded from https://biowardrobe.com/

At CCHMC Wardrobe experiment management system can only be accessed from within Cincinnati Children’s secure network (i.e. on site or via VPN) by authorized users. A laboratory group and laboratory administrator account can be set up with Artem Barski, PhD. Laboratory administrator account is allowed to add or remove users from the laboratory group and manage experiments records. To encourage collaboration, analyzed data track can be viewed on the UCSC genome browser, but not analyzed, by all accounts irrespective of whether that information has been placed in a shared folder (there is no anonymous access to Wardrobe).

Contributions and Acknowledgements

The Wardrobe software package and users’ guide were generated collaboratively by Artem Barski, PhD and Andrey V. Kartashov, MS. Editorial assistance was provided by Shawna Hottinger, MS.

Abbreviations

  • ATDP: average tag density profile
  • CCHMC: Cincinnati Children’s Hospital Medical Center
  • ChIP: chromatin immunoprecipitation
  • ChIP-Seq: chromatin immunoprecipitation sequencing
  • DESeq: differential gene expression analysis
  • DNA-Seq: deoxyribonucleic acid sequencing
  • ERCC: External RNA Control Consortium (ERCC), used in the context of an established set of RNA standards
  • FASTQ: a next-generation sequencing data format
  • MACS: model-based analysis of ChIP-Seq
  • MAnorm: a model for quantitative comparison of ChIP-Seq datasets
  • MWW: Mann-Whitney-Wilcoxon test
  • QC: quality control
  • RNA-Seq: ribonucleic acid sequencing
  • RPKM: reads per kilobase per million
  • Seq: sequencing
  • SRA: sequence read archive (previously known as short read archive), a type of data format
  • TSS: transcription start site(s)
  • VPN: virtual private network

Basic Analysis

Advanced Analysis

Wardrobe Settings