Saturday, January 15, 2011

A pipeline for RNA-seq data processing and quality assessment

A pipeline for RNA-seq data processing and quality assessment: "

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.


Contact: angela.goncalves@ebi.ac.uk

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(Via Bioinformatics - Advance Access.)