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

doi:10.1093/bioinformatics/bts023

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

Department of Computer Science & Engineering

Research output: Contribution to journal › Article › peer-review

62 Scopus citations

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.

Original language	English
Article number	bts023
Pages (from-to)	721-723
Number of pages	3
Journal	Bioinformatics
Volume	28
Issue number	5
DOIs	https://doi.org/10.1093/bioinformatics/bts023
State	Published - 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.

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title = "FX: An RNA-seq analysis tool on the cloud",

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.",

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

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.",

year = "2012",

month = mar,

doi = "10.1093/bioinformatics/bts023",

language = "English",

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pages = "721--723",

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AU - Ju, Young Seok

AU - Kim, Sujung

AU - Yu, Saet Byeol

AU - Bleazard, Thomas

AU - Park, Hyun Seok

AU - Rhee, Hwanseok

AU - Chong, Hyonyong

AU - Yang, Kap Seok

AU - Lee, Yeon Su

AU - Kim, In Hoo

AU - Lee, Jin Soo

AU - Kim, Jong Il

AU - Seo, Jeong Sun

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FX: An RNA-seq analysis tool on the cloud

Abstract

Bibliographical note

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