{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T20:33:41Z","timestamp":1768595621293,"version":"3.49.0"},"posted":{"date-parts":[[2014,6,6]]},"group-title":"Bioinformatics","reference-count":28,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2014,6,6]],"date-time":"2014-06-06T00:00:00Z","timestamp":1402012800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2014,6,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>RNA-sequencing (RNA-Seq) has become the technology of choice for whole-transcriptome profiling. However, processing the millions of sequence reads generated requires considerable bioinformatics skills and computational resources. At each step of the processing pipeline many tools are available, each with specific advantages and disadvantages. While using a specific combination of tools might be desirable, integrating the different tools can be time consuming, often due to specificities in the formats of input\/output files required by the different programs.<\/jats:p>\n                <jats:p>Here we present iRAP, an integrated RNA-seq analysis pipeline that allows the user to select and apply their preferred combination of existing tools for mapping reads, quantifying expression, testing for differential expression. iRAP also includes multiple tools for gene set enrichment analysis and generates web browsable reports of the results obtained in the different stages of the pipeline. Depending upon the application, iRAP can be used to quantify expression at the gene, exon or transcript level. iRAP is aimed at a broad group of users with basic bioinformatics training and requires little experience with the command line. Despite this, it also provides more advanced users with the ability to customise the options used by their chosen tools.<\/jats:p>\n                <jats:p>\n                  iRAP is available under General Public License 3 (GPLv3) and although it should be portable to any POSIX-compliant operating system, several third party programs only run on Linux. iRAP can be obtained from\n                  <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/code.google.com\/p\/irap\">http:\/\/code.google.com\/p\/irap<\/jats:ext-link>\n                  .\n                <\/jats:p>","DOI":"10.1101\/005991","type":"posted-content","created":{"date-parts":[[2014,6,6]],"date-time":"2014-06-06T23:36:21Z","timestamp":1402097781000},"source":"Crossref","is-referenced-by-count":25,"title":["iRAP - an integrated RNA-seq Analysis Pipeline"],"prefix":"10.64898","author":[{"given":"Nuno A.","family":"Fonseca","sequence":"first","affiliation":[]},{"given":"Robert","family":"Petryszak","sequence":"additional","affiliation":[]},{"given":"John C.","family":"Marioni","sequence":"additional","affiliation":[]},{"given":"Alvis","family":"Brazma","sequence":"additional","affiliation":[]}],"member":"54368","reference":[{"key":"2024080302082801000_005991v1.1","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2010-11-10-r106"},{"key":"2024080302082801000_005991v1.2","doi-asserted-by":"crossref","unstructured":"Simon Anders , Paul Theodor Pyl , and Wolfgang Huber . HTSeq\u2013A Python framework to work with high-throughput sequencing data. bioRxiv, 2014.","DOI":"10.1101\/002824"},{"key":"2024080302082801000_005991v1.3","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts635"},{"key":"2024080302082801000_005991v1.4","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts605"},{"key":"2024080302082801000_005991v1.5","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2010-11-8-r86"},{"key":"2024080302082801000_005991v1.6","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr012"},{"key":"2024080302082801000_005991v1.7","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts294"},{"key":"2024080302082801000_005991v1.8","doi-asserted-by":"crossref","unstructured":"Songbo Huang , Jinbo Zhang , Ruiqiang Li , Wenqian Zhang , Zengquan He , Tak-Wah Lam , Zhiyu Peng , and Siu-Ming Yiu . SOAPsplice: genome-wide ab initio detection of splice junctions from RNA-Seq data. Frontiers in Genetics, 2(0), 2011.","DOI":"10.3389\/fgene.2011.00046"},{"key":"2024080302082801000_005991v1.9","doi-asserted-by":"crossref","unstructured":"Daehwan Kim , Geo Pertea , Cole Trapnell , Harold Pimentel , Ryan Kelley , and Steven L Salzberg . Tophat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome biology, 14(4):R36, 2013.","DOI":"10.1186\/gb-2013-14-4-r36"},{"key":"2024080302082801000_005991v1.10","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt016"},{"key":"2024080302082801000_005991v1.11","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1923"},{"key":"2024080302082801000_005991v1.12","doi-asserted-by":"crossref","unstructured":"B. Langmead , C. Trapnell , M. Pop , S.L. Salzberg , et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol, 10(3):R25, 2009.","DOI":"10.1186\/gb-2009-10-3-r25"},{"key":"2024080302082801000_005991v1.13","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp324"},{"key":"2024080302082801000_005991v1.14","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp698"},{"key":"2024080302082801000_005991v1.15","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp352"},{"key":"2024080302082801000_005991v1.16","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-14-220"},{"issue":"12","key":"2024080302082801000_005991v1.17","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.1038\/nmeth.2221","article-title":"The GEM mapper: fast, accurate and versatile alignment by filtration","volume":"9","year":"2012","journal-title":"Nature Methods"},{"key":"2024080302082801000_005991v1.18","doi-asserted-by":"publisher","DOI":"10.1038\/nature08903"},{"key":"2024080302082801000_005991v1.19","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp616"},{"key":"2024080302082801000_005991v1.20","doi-asserted-by":"crossref","unstructured":"Wandaliz Torres-Garc\u00eda , Siyuan Zheng , Andrey Sivachenko , Rahulsimham Vegesna , Qianghu Wang , Rong Yao , Michael F Berger , John N Weinstein , Gad Getz , and Roel GW Verhaak . Prada: Pipeline for rna sequencing data analysis. Bioinformatics, page btu169, 2014.","DOI":"10.1093\/bioinformatics\/btu169"},{"key":"2024080302082801000_005991v1.21","doi-asserted-by":"crossref","unstructured":"C. Trapnell , D.G. Hendrickson , M. Sauvageau , L. Goff , J.L. Rinn , and L. Pachter . Differential analysis of gene regulation at transcript resolution with rna-seq. Nature Biotechnology, 2012.","DOI":"10.1038\/nbt.2450"},{"key":"2024080302082801000_005991v1.22","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp120"},{"key":"2024080302082801000_005991v1.23","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.1621"},{"key":"2024080302082801000_005991v1.24","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2012.016"},{"key":"2024080302082801000_005991v1.25","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2011-12-2-r13"},{"key":"2024080302082801000_005991v1.26","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkt111"},{"key":"2024080302082801000_005991v1.27","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr441"},{"key":"2024080302082801000_005991v1.28","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq057"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/005991","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,14]],"date-time":"2026-01-14T22:06:15Z","timestamp":1768428375000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/005991"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,6,6]]},"references-count":28,"URL":"https:\/\/doi.org\/10.1101\/005991","relation":{},"subject":[],"published":{"date-parts":[[2014,6,6]]},"subtype":"preprint"}}