Display Settings:

Format

Send to:

Choose Destination
See comment in PubMed Commons below
Bioinformatics. 2011 Mar 15;27(6):867-9. doi: 10.1093/bioinformatics/btr012. Epub 2011 Jan 13.

A pipeline for RNA-seq data processing and quality assessment.

Author information

  • 1EMBL Outstation-Hinxton, European Bioinformatics Institute, Cambridge, UK. angela.goncalves@ebi.ac.uk

Abstract

SUMMARY:

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.

AVAILABILITY:

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.

PMID:
21233166
[PubMed - indexed for MEDLINE]
PMCID:
PMC3051320
Free PMC Article

Images from this publication.See all images (1)Free text

Fig. 1.
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Icon for HighWire Icon for PubMed Central
    Loading ...
    Write to the Help Desk