Dataset Information
A pipeline for RNA-seq data processing and quality assessment.
Ontology highlight
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.
SUBMITTER: Goncalves A
PROVIDER: S-EPMC3051320 | biostudies-literature | 2011 Mar
REPOSITORIES: biostudies-literature
Publications
A pipeline for RNA-seq data processing and quality assessment.
Bioinformatics (Oxford, England) 20110113 6
<h4>Summary</h4>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-clo ...[more]