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A pipeline for RNA-seq data processing and quality assessment.
Bioinformatics. 2011 Jan 13;
Authors: Goncalves A, Tikhonov A, Brazma A, Kapushesky M
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: [email protected].
PMID: 21233166 [PubMed - as supplied by publisher]
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A pipeline for RNA-seq data processing and quality assessment.
Bioinformatics. 2011 Jan 13;
Authors: Goncalves A, Tikhonov A, Brazma A, Kapushesky M
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: [email protected].
PMID: 21233166 [PubMed - as supplied by publisher]
More...