Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

iRAP - an integrated RNA-seq Analysis Pipeline

Nuno A. Fonseca, Robert Petryszak, John C. Marioni, Alvis Brazma
doi: https://doi.org/10.1101/005991
Nuno A. Fonseca
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Robert Petryszak
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
John C. Marioni
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Alvis Brazma
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

RNA-sequencing (RNA-Seq) has become the technology of choice for whole-transcriptome profiling. However, processing the millions of sequence reads generated requires considerable bioinformatics skills and computational resources. At each step of the processing pipeline many tools are available, each with specific advantages and disadvantages. While using a specific combination of tools might be desirable, integrating the different tools can be time consuming, often due to specificities in the formats of input/output files required by the different programs.

Here we present iRAP, an integrated RNA-seq analysis pipeline that allows the user to select and apply their preferred combination of existing tools for mapping reads, quantifying expression, testing for differential expression. iRAP also includes multiple tools for gene set enrichment analysis and generates web browsable reports of the results obtained in the different stages of the pipeline. Depending upon the application, iRAP can be used to quantify expression at the gene, exon or transcript level. iRAP is aimed at a broad group of users with basic bioinformatics training and requires little experience with the command line. Despite this, it also provides more advanced users with the ability to customise the options used by their chosen tools.

iRAP is available under General Public License 3 (GPLv3) and although it should be portable to any POSIX-compliant operating system, several third party programs only run on Linux. iRAP can be obtained from http://code.google.com/p/irap.

Footnotes

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted June 06, 2014.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
iRAP - an integrated RNA-seq Analysis Pipeline
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
iRAP - an integrated RNA-seq Analysis Pipeline
Nuno A. Fonseca, Robert Petryszak, John C. Marioni, Alvis Brazma
bioRxiv 005991; doi: https://doi.org/10.1101/005991
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
iRAP - an integrated RNA-seq Analysis Pipeline
Nuno A. Fonseca, Robert Petryszak, John C. Marioni, Alvis Brazma
bioRxiv 005991; doi: https://doi.org/10.1101/005991

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Bioinformatics
Subject Areas
All Articles
  • Animal Behavior and Cognition (4672)
  • Biochemistry (10337)
  • Bioengineering (7655)
  • Bioinformatics (26286)
  • Biophysics (13497)
  • Cancer Biology (10666)
  • Cell Biology (15408)
  • Clinical Trials (138)
  • Developmental Biology (8485)
  • Ecology (12803)
  • Epidemiology (2067)
  • Evolutionary Biology (16821)
  • Genetics (11381)
  • Genomics (15461)
  • Immunology (10596)
  • Microbiology (25165)
  • Molecular Biology (10197)
  • Neuroscience (54382)
  • Paleontology (399)
  • Pathology (1665)
  • Pharmacology and Toxicology (2889)
  • Physiology (4332)
  • Plant Biology (9234)
  • Scientific Communication and Education (1585)
  • Synthetic Biology (2554)
  • Systems Biology (6770)
  • Zoology (1461)