{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,16]],"date-time":"2026-02-16T08:35:25Z","timestamp":1771230925902,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"15","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: \u2003Technological advances in high-throughput sequencing necessitate improved computational tools for processing and analyzing large-scale datasets in a systematic automated manner. For that purpose, we have developed PRADA (Pipeline for RNA-Sequencing Data Analysis), a flexible, modular and highly scalable software platform that provides many different types of information available by multifaceted analysis starting from raw paired-end RNA-seq data: gene expression levels, quality metrics, detection of unsupervised and supervised fusion transcripts, detection of intragenic fusion variants, homology scores and fusion frame classification. PRADA uses a dual-mapping strategy that increases sensitivity and refines the analytical endpoints. PRADA has been used extensively and successfully in the glioblastoma and renal clear cell projects of The Cancer Genome Atlas program.<\/jats:p>\n               <jats:p>Availability and implementation: \u2003 http:\/\/sourceforge.net\/projects\/prada\/<\/jats:p>\n               <jats:p>Contact: \u2003 gadgetz@broadinstitute.org or rverhaak@mdanderson.org<\/jats:p>\n               <jats:p>Supplementary information: \u2003 Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu169","type":"journal-article","created":{"date-parts":[[2014,4,3]],"date-time":"2014-04-03T01:29:50Z","timestamp":1396488590000},"page":"2224-2226","source":"Crossref","is-referenced-by-count":150,"title":["PRADA: pipeline for RNA sequencing data analysis"],"prefix":"10.1093","volume":"30","author":[{"given":"Wandaliz","family":"Torres-Garc\u00eda","sequence":"first","affiliation":[{"name":"1 Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, 2 The Eli and Edythe L. Broad Institute of Harvard University and MIT, Cambridge, MA 02142 and 3 Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY 10015, USA"}]},{"given":"Siyuan","family":"Zheng","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, 2 The Eli and Edythe L. Broad Institute of Harvard University and MIT, Cambridge, MA 02142 and 3 Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY 10015, USA"}]},{"given":"Andrey","family":"Sivachenko","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, 2 The Eli and Edythe L. Broad Institute of Harvard University and MIT, Cambridge, MA 02142 and 3 Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY 10015, USA"}]},{"given":"Rahulsimham","family":"Vegesna","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, 2 The Eli and Edythe L. Broad Institute of Harvard University and MIT, Cambridge, MA 02142 and 3 Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY 10015, USA"}]},{"given":"Qianghu","family":"Wang","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, 2 The Eli and Edythe L. Broad Institute of Harvard University and MIT, Cambridge, MA 02142 and 3 Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY 10015, USA"}]},{"given":"Rong","family":"Yao","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, 2 The Eli and Edythe L. Broad Institute of Harvard University and MIT, Cambridge, MA 02142 and 3 Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY 10015, USA"}]},{"given":"Michael F.","family":"Berger","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, 2 The Eli and Edythe L. Broad Institute of Harvard University and MIT, Cambridge, MA 02142 and 3 Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY 10015, USA"}]},{"given":"John N.","family":"Weinstein","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, 2 The Eli and Edythe L. Broad Institute of Harvard University and MIT, Cambridge, MA 02142 and 3 Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY 10015, USA"}]},{"given":"Gad","family":"Getz","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, 2 The Eli and Edythe L. Broad Institute of Harvard University and MIT, Cambridge, MA 02142 and 3 Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY 10015, USA"}]},{"given":"Roel G.W.","family":"Verhaak","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, 2 The Eli and Edythe L. Broad Institute of Harvard University and MIT, Cambridge, MA 02142 and 3 Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY 10015, USA"}]}],"member":"286","published-online":{"date-parts":[[2014,4,1]]},"reference":[{"key":"2023012711521642300_btu169-B1","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1101\/gr.103697.109","article-title":"Integrative analysis of the melanoma transcriptome","volume":"20","author":"Berger","year":"2010","journal-title":"Genome Res"},{"key":"2023012711521642300_btu169-B2","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1038\/nature12222","article-title":"Comprehensive molecular characterization of clear cell renal cell carcinoma","volume":"499","author":"Cancer Genome Atlas Research Network","year":"2013","journal-title":"Nature"},{"key":"2023012711521642300_btu169-B3","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1093\/bioinformatics\/bts196","article-title":"RNA-SeQC: RNA-seq metrics for quality control and process optimization","volume":"28","author":"DeLuca","year":"2012","journal-title":"Bioinformatics"},{"key":"2023012711521642300_btu169-B4","doi-asserted-by":"crossref","first-page":"998","DOI":"10.1038\/nature06742","article-title":"Genotype, haplotype and copy-number variation in worldwide human populations","volume":"451","author":"Jakobsson","year":"2008","journal-title":"Nature"},{"key":"2023012711521642300_btu169-B5","doi-asserted-by":"crossref","first-page":"R72","DOI":"10.1186\/gb-2011-12-8-r72","article-title":"TopHat-Fusion: an algorithm for discovery of novel fusion transcripts","volume":"12","author":"Kim","year":"2012","journal-title":"Genome Biol."},{"key":"2023012711521642300_btu169-B6","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":"2023012711521642300_btu169-B7","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012711521642300_btu169-B8","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Res."},{"key":"2023012711521642300_btu169-B9","doi-asserted-by":"crossref","first-page":"e1001138","DOI":"10.1371\/journal.pcbi.1001138","article-title":"deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data","volume":"7","author":"McPherson","year":"2011","journal-title":"PLoS Comput. 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