title: FX: an RNA-Seq analysis tool on the cloud.
abstract: FX is an RNA-Seq analysis tool, which runs in parallel on cloud computing infrastructure, for the estimation of gene expression levels and genomic variant calling. In the mapping of short RNA-Seq reads, FX uses a transcriptome-based reference primarily, generated from ~160 000 mRNA sequences from RefSeq, UCSC and Ensembl databases. This approach reduces the misalignment of reads originating from splicing junctions. Unmapped reads not aligned on known transcripts are then mapped on the human genome reference. FX allows analysis of RNA-Seq data on cloud computing infrastructures, supporting access through a user-friendly web interface.
  
  
  BACKGROUND
  FX is freely available on the web at (http://fx.gmi.ac.kr), and can be installed on local Hadoop clusters. Guidance for the installation and operation of FX can be found under the 'Documentation' menu on the website.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul.
authors.forename: Dongwan
authors.initials: D
authors.lastname: Hong
authors.forename: Arang
authors.initials: A
authors.lastname: Rhie
authors.forename: Sung-Soo
authors.initials: SS
authors.lastname: Park
authors.forename: Jongkeun
authors.initials: J
authors.lastname: Lee
authors.forename: Young Seok
authors.initials: YS
authors.lastname: Ju
authors.forename: Sujung
authors.initials: S
authors.lastname: Kim
authors.forename: Saet-Byeol
authors.initials: SB
authors.lastname: Yu
authors.forename: Thomas
authors.initials: T
authors.lastname: Bleazard
authors.forename: Hyun-Seok
authors.initials: HS
authors.lastname: Park
authors.forename: Hwanseok
authors.initials: H
authors.lastname: Rhee
authors.forename: Hyonyong
authors.initials: H
authors.lastname: Chong
authors.forename: Kap-Seok
authors.initials: KS
authors.lastname: Yang
authors.forename: Yeon-Su
authors.initials: YS
authors.lastname: Lee
authors.forename: In-Hoo
authors.initials: IH
authors.lastname: Kim
authors.forename: Jin Soo
authors.initials: JS
authors.lastname: Lee
authors.forename: Jong-Il
authors.initials: JI
authors.lastname: Kim
authors.forename: Jeong-Sun
authors.initials: JS
authors.lastname: Seo
mesh_terms: D020869:Gene Expression Profiling; D016678:Genome; D015894:Genome, Human; D006801:Humans; D022821:RNA Splice Sites; D012326:RNA Splicing; D012333:RNA, Messenger / Q000235:genetics; D017423:Sequence Analysis, RNA; D014584:User-Computer Interface
chemical_list: D022821:RNA Splice Sites; D012333:RNA, Messenger