Introduction

We present an R based pipeline, ArrayExpressHTS, for pre-processing, expression estimation and data quality assessment of high-throughput sequencing transcriptional profiling (RNA-seq) datasets. The pipeline starts from raw sequence files and produces standard Bioconductor R objects containing gene or transcript measurements for downstream analysis along with web reports for data quality assessment. It may be run locally on a user's own computer or remotely on a distributed R-cloud farm at the European Bioinformatics Institute. It can be used to analyse user's own datasets or public RNA-seq datasets from the ArrayExpress Archive.The R package is available at www.ebi.ac.uk/tools/rcloud with online documentation at www.ebi.ac.uk/Tools/rwiki/, also available as supplementary material.

Publications

  1. A pipeline for RNA-seq data processing and quality assessment.
    Cite this
    Goncalves A, Tikhonov A, Brazma A, Kapushesky M, 2011-03-01 - Bioinformatics (Oxford, England)

Credits

  1. Angela Goncalves
    Developer

    EMBL Outstation-Hinxton, European Bioinformatics Institute

  2. Andrew Tikhonov
    Developer

  3. Alvis Brazma
    Developer

  4. Misha Kapushesky
    Investigator

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Summary
AccessionBT001537
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Submitted ByMisha Kapushesky