Octopus-toolkit: a workflow to automate mining of public epigenomic and transcriptomic next-generation sequencing data

Cited 41 time in webofscience Cited 0 time in scopus
  • Hit : 509
  • Download : 38
DC FieldValueLanguage
dc.contributor.authorKim, Taemookko
dc.contributor.authorSeo, Hogyu Davidko
dc.contributor.authorHennighausen, Lotharko
dc.contributor.authorLee, Daeyoupko
dc.contributor.authorKang, Keunsooko
dc.date.accessioned2018-06-16T07:37:24Z-
dc.date.available2018-06-16T07:37:24Z-
dc.date.created2018-06-11-
dc.date.created2018-06-11-
dc.date.created2018-06-11-
dc.date.created2018-06-11-
dc.date.created2018-06-11-
dc.date.created2018-06-11-
dc.date.issued2018-05-
dc.identifier.citationNUCLEIC ACIDS RESEARCH, v.46, no.9-
dc.identifier.issn0305-1048-
dc.identifier.urihttp://hdl.handle.net/10203/242542-
dc.description.abstractOctopus-toolkit is a stand-alone application for retrieving and processing large sets of next-generation sequencing (NGS) data with a single step. Octopus-toolkit is an automated set-up-and-analysis pipeline utilizing the Aspera, SRA Toolkit, FastQC, Trimmomatic, HISAT2, STAR, Samtools, and HOMER applications. All the applications are installed on the user's computer when the program starts. Upon the installation, it can automatically retrieve original files of various epigenomic and transcriptomic data sets, including ChIP-seq, ATAC-seq, DNase-seq, MeDIP-seq, MNase-seq and RNA-seq, from the gene expression omnibus data repository. The downloaded files can then be sequentially processed to generate BAM and BigWig files, which are used for advanced analyses and visualization. Currently, it can process NGS data from popular model genomes such as, human (Homo sapiens), mouse (Mus musculus), dog (Canis lupus familiaris), plant (Arabidopsis thaliana), zebrafish (Danio rerio), fruit fly (Drosophila melanogaster), worm (Caenorhabditis elegans), and budding yeast (Saccharomyces cerevisiae) genomes. With the processed files from Octopus-toolkit, the meta-analysis of various data sets, motif searches for DNA-binding proteins, and the identification of differentially expressed genes and/or protein-binding sites can be easily conducted with few commands by users. Overall, Octopus-toolkit facilitates the systematic and integrative analysis of available epigenomic and transcriptomic NGS big data.-
dc.languageEnglish-
dc.publisherOXFORD UNIV PRESS-
dc.titleOctopus-toolkit: a workflow to automate mining of public epigenomic and transcriptomic next-generation sequencing data-
dc.typeArticle-
dc.identifier.wosid000433056900002-
dc.identifier.scopusid2-s2.0-85047019870-
dc.type.rimsART-
dc.citation.volume46-
dc.citation.issue9-
dc.citation.publicationnameNUCLEIC ACIDS RESEARCH-
dc.identifier.doi10.1093/nar/gky083-
dc.embargo.liftdate9999-12-31-
dc.embargo.terms9999-12-31-
dc.contributor.localauthorLee, Daeyoup-
dc.contributor.nonIdAuthorHennighausen, Lothar-
dc.contributor.nonIdAuthorKang, Keunsoo-
dc.description.isOpenAccessY-
dc.type.journalArticleArticle-
dc.subject.keywordPlusSACCHAROMYCES-CEREVISIAE-
dc.subject.keywordPlusHUMAN GENOME-
dc.subject.keywordPlusRNA-SEQ-
dc.subject.keywordPlusCHROMATIN-
dc.subject.keywordPlusALIGNER-
dc.subject.keywordPlusGENES-
dc.subject.keywordPlusSTAT5-
Appears in Collection
BS-Journal Papers(저널논문)
Files in This Item
This item is cited by other documents in WoS
⊙ Detail Information in WoSⓡ Click to see webofscience_button
⊙ Cited 41 items in WoS Click to see citing articles in records_button

qr_code

  • mendeley

    citeulike


rss_1.0 rss_2.0 atom_1.0