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 with online documentation at, also available as supplementary material.



(Via Bioinformatics - Advance Access.)