{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,28]],"date-time":"2026-01-28T00:41:59Z","timestamp":1769560919958,"version":"3.49.0"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: We have developed an RNA-Seq analysis workflow for single-ended Illumina reads, termed RseqFlow. This workflow includes a set of analytic functions, such as quality control for sequencing data, signal tracks of mapped reads, calculation of expression levels, identification of differentially expressed genes and coding SNPs calling. This workflow is formalized and managed by the Pegasus Workflow Management System, which maps the analysis modules onto available computational resources, automatically executes the steps in the appropriate order and supervises the whole running process. RseqFlow is available as a Virtual Machine with all the necessary software, which eliminates any complex configuration and installation steps.<\/jats:p>\n               <jats:p>Availability and implementation: \u00a0http:\/\/genomics.isi.edu\/rnaseq<\/jats:p>\n               <jats:p>Contact: \u00a0wangying@xmu.edu.cn; knowles@med.usc.edu; deelman@isi.edu; tingchen@usc.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr441","type":"journal-article","created":{"date-parts":[[2011,7,28]],"date-time":"2011-07-28T03:11:47Z","timestamp":1311822707000},"page":"2598-2600","source":"Crossref","is-referenced-by-count":27,"title":["RseqFlow: workflows for RNA-Seq data analysis"],"prefix":"10.1093","volume":"27","author":[{"given":"Ying","family":"Wang","sequence":"first","affiliation":[{"name":"1 Department of Biological Sciences, USC, 1050 Childs Way, Los Angeles, CA 90089, USA, 2Department of Automation, Xiamen University, China, 3USC Information Sciences Institute, 4676 Admiralty Way, Marina del Rey, CA 90292, USA and 4USC Keck School of Medicine, Department of Psychiatry, 1501 San Pablo St., Los Angeles, CA 90033, USA"},{"name":"1 Department of Biological Sciences, USC, 1050 Childs Way, Los Angeles, CA 90089, USA, 2Department of Automation, Xiamen University, China, 3USC Information Sciences Institute, 4676 Admiralty Way, Marina del Rey, CA 90292, USA and 4USC Keck School of Medicine, Department of Psychiatry, 1501 San Pablo St., Los Angeles, CA 90033, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gaurang","family":"Mehta","sequence":"additional","affiliation":[{"name":"1 Department of Biological Sciences, USC, 1050 Childs Way, Los Angeles, CA 90089, USA, 2Department of Automation, Xiamen University, China, 3USC Information Sciences Institute, 4676 Admiralty Way, Marina del Rey, CA 90292, USA and 4USC Keck School of Medicine, Department of Psychiatry, 1501 San Pablo St., Los Angeles, CA 90033, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rajiv","family":"Mayani","sequence":"additional","affiliation":[{"name":"1 Department of Biological Sciences, USC, 1050 Childs Way, Los Angeles, CA 90089, USA, 2Department of Automation, Xiamen University, China, 3USC Information Sciences Institute, 4676 Admiralty Way, Marina del Rey, CA 90292, USA and 4USC Keck School of Medicine, Department of Psychiatry, 1501 San Pablo St., Los Angeles, CA 90033, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jingxi","family":"Lu","sequence":"additional","affiliation":[{"name":"1 Department of Biological Sciences, USC, 1050 Childs Way, Los Angeles, CA 90089, USA, 2Department of Automation, Xiamen University, China, 3USC Information Sciences Institute, 4676 Admiralty Way, Marina del Rey, CA 90292, USA and 4USC Keck School of Medicine, Department of Psychiatry, 1501 San Pablo St., Los Angeles, CA 90033, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tade","family":"Souaiaia","sequence":"additional","affiliation":[{"name":"1 Department of Biological Sciences, USC, 1050 Childs Way, Los Angeles, CA 90089, USA, 2Department of Automation, Xiamen University, China, 3USC Information Sciences Institute, 4676 Admiralty Way, Marina del Rey, CA 90292, USA and 4USC Keck School of Medicine, Department of Psychiatry, 1501 San Pablo St., Los Angeles, CA 90033, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yangho","family":"Chen","sequence":"additional","affiliation":[{"name":"1 Department of Biological Sciences, USC, 1050 Childs Way, Los Angeles, CA 90089, USA, 2Department of Automation, Xiamen University, China, 3USC Information Sciences Institute, 4676 Admiralty Way, Marina del Rey, CA 90292, USA and 4USC Keck School of Medicine, Department of Psychiatry, 1501 San Pablo St., Los Angeles, CA 90033, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrew","family":"Clark","sequence":"additional","affiliation":[{"name":"1 Department of Biological Sciences, USC, 1050 Childs Way, Los Angeles, CA 90089, USA, 2Department of Automation, Xiamen University, China, 3USC Information Sciences Institute, 4676 Admiralty Way, Marina del Rey, CA 90292, USA and 4USC Keck School of Medicine, Department of Psychiatry, 1501 San Pablo St., Los Angeles, CA 90033, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hee Jae","family":"Yoon","sequence":"additional","affiliation":[{"name":"1 Department of Biological Sciences, USC, 1050 Childs Way, Los Angeles, CA 90089, USA, 2Department of Automation, Xiamen University, China, 3USC Information Sciences Institute, 4676 Admiralty Way, Marina del Rey, CA 90292, USA and 4USC Keck School of Medicine, Department of Psychiatry, 1501 San Pablo St., Los Angeles, CA 90033, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lin","family":"Wan","sequence":"additional","affiliation":[{"name":"1 Department of Biological Sciences, USC, 1050 Childs Way, Los Angeles, CA 90089, USA, 2Department of Automation, Xiamen University, China, 3USC Information Sciences Institute, 4676 Admiralty Way, Marina del Rey, CA 90292, USA and 4USC Keck School of Medicine, Department of Psychiatry, 1501 San Pablo St., Los Angeles, CA 90033, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Oleg V.","family":"Evgrafov","sequence":"additional","affiliation":[{"name":"1 Department of Biological Sciences, USC, 1050 Childs Way, Los Angeles, CA 90089, USA, 2Department of Automation, Xiamen University, China, 3USC Information Sciences Institute, 4676 Admiralty Way, Marina del Rey, CA 90292, USA and 4USC Keck School of Medicine, Department of Psychiatry, 1501 San Pablo St., Los Angeles, CA 90033, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James A.","family":"Knowles","sequence":"additional","affiliation":[{"name":"1 Department of Biological Sciences, USC, 1050 Childs Way, Los Angeles, CA 90089, USA, 2Department of Automation, Xiamen University, China, 3USC Information Sciences Institute, 4676 Admiralty Way, Marina del Rey, CA 90292, USA and 4USC Keck School of Medicine, Department of Psychiatry, 1501 San Pablo St., Los Angeles, CA 90033, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ewa","family":"Deelman","sequence":"additional","affiliation":[{"name":"1 Department of Biological Sciences, USC, 1050 Childs Way, Los Angeles, CA 90089, USA, 2Department of Automation, Xiamen University, China, 3USC Information Sciences Institute, 4676 Admiralty Way, Marina del Rey, CA 90292, USA and 4USC Keck School of Medicine, Department of Psychiatry, 1501 San Pablo St., Los Angeles, CA 90033, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ting","family":"Chen","sequence":"additional","affiliation":[{"name":"1 Department of Biological Sciences, USC, 1050 Childs Way, Los Angeles, CA 90089, USA, 2Department of Automation, Xiamen University, China, 3USC Information Sciences Institute, 4676 Admiralty Way, Marina del Rey, CA 90292, USA and 4USC Keck School of Medicine, Department of Psychiatry, 1501 San Pablo St., Los Angeles, CA 90033, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,7,27]]},"reference":[{"key":"2023012512002775900_B1","doi-asserted-by":"crossref","first-page":"R106","DOI":"10.1186\/gb-2010-11-10-r106","article-title":"Differential expression analysis for sequence count data","volume":"11","author":"Anders","year":"2010","journal-title":"Genome Biol."},{"key":"2023012512002775900_B2","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1016\/j.jcss.2009.11.005","article-title":"Scaling up workflow-based applications","volume":"76","author":"Callaghan","year":"2010","journal-title":"J. Comput. Syst. Sci."},{"key":"2023012512002775900_B3","doi-asserted-by":"crossref","first-page":"2514","DOI":"10.1093\/bioinformatics\/btp486","article-title":"PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds","volume":"25","author":"Chen","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012512002775900_B4","first-page":"219","article-title":"Pegasus: a framework for mapping complex scientific workflows onto distributed systems","volume":"13","author":"Deelman","year":"2005","journal-title":"Sci. Program. J."},{"key":"2023012512002775900_B5","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1007\/978-1-84628-757-2_23","article-title":"Pegasus: mapping large-scale workflows to distributed resources","volume-title":"Workflows for e-Science","author":"Deelman","year":"2007"},{"key":"2023012512002775900_B6","doi-asserted-by":"crossref","first-page":"867","DOI":"10.1093\/bioinformatics\/btr012","article-title":"A pipeline for RNA-seq data processing and quality assessment","volume":"27","author":"Goncalves","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012512002775900_B7","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1093\/bioinformatics\/btq643","article-title":"RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries","volume":"27","author":"Habegger","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012512002775900_B8","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1093\/bioinformatics\/btp113","article-title":"Statistical inferences for isoform expression in RNA-Seq","volume":"25","author":"Jiang","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012512002775900_B9","doi-asserted-by":"crossref","DOI":"10.1109\/SC.2010.17","article-title":"Data sharing options for scientific workflows on Amazon EC2","volume-title":"Proceedings of the 2010 ACM\/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis","author":"Juve","year":"2010"},{"key":"2023012512002775900_B10","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"Langmead","year":"2009","journal-title":"Genome Biol."},{"key":"2023012512002775900_B11","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012512002775900_B12","doi-asserted-by":"crossref","first-page":"1509","DOI":"10.1101\/gr.079558.108","article-title":"RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays","volume":"18","author":"Marioni","year":"2008","journal-title":"Genome Res."},{"key":"2023012512002775900_B13","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1038\/nmeth.1226","article-title":"Mapping and quantifying mammalian transcriptomes by RNA-Seq","volume":"5","author":"Mortazavi","year":"2008","journal-title":"Nature Method"},{"key":"2023012512002775900_B14","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1093\/bioinformatics\/btp615","article-title":"inGAP: an integrated next-generation genome analysis pipeline","volume":"26","author":"Qi","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012512002775900_B15","doi-asserted-by":"crossref","first-page":"e170","DOI":"10.1093\/nar\/gkq670","article-title":"A two-parameter generalized Poisson model to improve the analysis of RNA-seq data","volume":"38","author":"Srivastava","year":"2010","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/18\/2598\/48865010\/bioinformatics_27_18_2598.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/18\/2598\/48865010\/bioinformatics_27_18_2598.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T13:49:37Z","timestamp":1674654577000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/18\/2598\/181908"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,7,27]]},"references-count":15,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2011,9,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr441","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,9,15]]},"published":{"date-parts":[[2011,7,27]]}}}