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- Title
A pipeline for RNA-seq data processing and quality assessment.
- Authors
Goncalves, Angela; Tikhonov, Andrew; Brazma, Alvis; Kapushesky, Misha
- Abstract
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.
- Publication
Bioinformatics (Oxford, England), 2011, Vol 27, Issue 6, p867
- ISSN
1367-4811
- Publication type
Journal Article
- DOI
10.1093/bioinformatics/btr012