FX: An RNA-seq analysis tool on the cloud

Dongwan Hong, Arang Rhie, Sung Soo Park, Jongkeun Lee, Young Seok Ju, Sujung Kim, Saet Byeol Yu, Thomas Bleazard, Hyun Seok Park, Hwanseok Rhee, Hyonyong Chong, Kap Seok Yang, Yeon Su Lee, In Hoo Kim, Jin Soo Lee, Jong Il Kim, Jeong Sun Seo

Research output: Contribution to journalArticlepeer-review

62 Scopus citations


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.

Original languageEnglish
Article numberbts023
Pages (from-to)721-723
Number of pages3
Issue number5
StatePublished - Mar 2012

Bibliographical note

Funding Information:
Funding: Green Cross Therapeutics (grant No. 0411-20080023 to J.-S.S.); Korean Ministry of Knowledge Economy (grant No. 10037410-2011-02 to J.-S.S.); Korean Ministry of Education, Science, Technology (grant No. M10305030000 to J.-S.S.; grant No. 2010-0013662 to J.-I.K.); Small Medium Business Administration (grant No. 000358780109 to H.-S.P.); Amazon Web Services (June 2011 EDU research award) in part.


Dive into the research topics of 'FX: An RNA-seq analysis tool on the cloud'. Together they form a unique fingerprint.

Cite this