title: A pipeline for RNA-seq data processing and quality assessment.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  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.
authors.affiliation: EMBL Outstation-Hinxton, European Bioinformatics Institute, Cambridge, UK. angela.goncalves@ebi.ac.uk
authors.forename: Angela
authors.initials: A
authors.lastname: Goncalves
authors.forename: Andrew
authors.initials: A
authors.lastname: Tikhonov
authors.forename: Alvis
authors.initials: A
authors.lastname: Brazma
authors.forename: Misha
authors.initials: M
authors.lastname: Kapushesky
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods; D020407:Internet; D012313:RNA / Q000032:analysis; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D012313:RNA