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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
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Robert Petryszak
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
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John C. Marioni
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
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Alvis Brazma
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
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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.

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    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.
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    Posted June 06, 2014.
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    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
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    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

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