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- Title
FX: an RNA-Seq analysis tool on the cloud.
- Authors
Hong, Dongwan; Rhie, Arang; Park, Sung-Soo; Lee, Jongkeun; Ju, Young Seok; Kim, Sujung; Yu, Saet-Byeol; Bleazard, Thomas; Park, Hyun-Seok; Rhee, Hwanseok; Chong, Hyonyong; Yang, Kap-Seok; Lee, Yeon-Su; Kim, In-Hoo; Lee, Jin Soo; Kim, Jong-Il; Seo, Jeong-Sun
- Abstract
Summary: 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.Availability: 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.Contact: jeongsun@snu.ac.kr; jongil@snu.ac.krSupplementary information: Supplementary data are available at Bioinformatics online.
- Subjects
NUCLEOTIDE sequence; CLOUD computing; ESTIMATION theory; GENE expression; RNA splicing; HUMAN genome; COMPUTATIONAL biology
- Publication
Bioinformatics, 2012, Vol 28, Issue 5, p721
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/bts023