{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T02:19:29Z","timestamp":1775787569816,"version":"3.50.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2128,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The advent of next-generation sequencing for functional genomics has given rise to quantities of sequence information that are often so large that they are difficult to handle. Moreover, sequence reads from a specific individual can contain sufficient information to potentially identify and genetically characterize that person, raising privacy concerns. In order to address these issues, we have developed the Mapped Read Format (MRF), a compact data summary format for both short and long read alignments that enables the anonymization of confidential sequence information, while allowing one to still carry out many functional genomics studies. We have developed a suite of tools (RSEQtools) that use this format for the analysis of RNA-Seq experiments. These tools consist of a set of modules that perform common tasks such as calculating gene expression values, generating signal tracks of mapped reads and segmenting that signal into actively transcribed regions. Moreover, the tools can readily be used to build customizable RNA-Seq workflows. In addition to the anonymization afforded by MRF, this format also facilitates the decoupling of the alignment of reads from downstream analyses.<\/jats:p>\n               <jats:p>Availability and implementation: RSEQtools is implemented in C and the source code is available at http:\/\/rseqtools.gersteinlab.org\/.<\/jats:p>\n               <jats:p>Contact: \u00a0lukas.habegger@yale.edu; mark.gerstein@yale.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq643","type":"journal-article","created":{"date-parts":[[2010,12,7]],"date-time":"2010-12-07T04:48:21Z","timestamp":1291697301000},"page":"281-283","source":"Crossref","is-referenced-by-count":97,"title":["RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries"],"prefix":"10.1093","volume":"27","author":[{"given":"Lukas","family":"Habegger","sequence":"first","affiliation":[{"name":"1 Program in Computational Biology and Bioinformatics, 2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 3Wyss Institute for Biologically-Inspired Engineering at Harvard, Boston, MA, 4Department of Genetics, Harvard Medical School, Boston, MA, 5Department of Computer Science, Yale University, New Haven, CT and 6Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA"},{"name":"1 Program in Computational Biology and Bioinformatics, 2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 3Wyss Institute for Biologically-Inspired Engineering at Harvard, Boston, MA, 4Department of Genetics, Harvard Medical School, Boston, MA, 5Department of Computer Science, Yale University, New Haven, CT and 6Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrea","family":"Sboner","sequence":"additional","affiliation":[{"name":"1 Program in Computational Biology and Bioinformatics, 2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 3Wyss Institute for Biologically-Inspired Engineering at Harvard, Boston, MA, 4Department of Genetics, Harvard Medical School, Boston, MA, 5Department of Computer Science, Yale University, New Haven, CT and 6Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA"},{"name":"1 Program in Computational Biology and Bioinformatics, 2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 3Wyss Institute for Biologically-Inspired Engineering at Harvard, Boston, MA, 4Department of Genetics, Harvard Medical School, Boston, MA, 5Department of Computer Science, Yale University, New Haven, CT and 6Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tara A.","family":"Gianoulis","sequence":"additional","affiliation":[{"name":"1 Program in Computational Biology and Bioinformatics, 2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 3Wyss Institute for Biologically-Inspired Engineering at Harvard, Boston, MA, 4Department of Genetics, Harvard Medical School, Boston, MA, 5Department of Computer Science, Yale University, New Haven, CT and 6Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA"},{"name":"1 Program in Computational Biology and Bioinformatics, 2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 3Wyss Institute for Biologically-Inspired Engineering at Harvard, Boston, MA, 4Department of Genetics, Harvard Medical School, Boston, MA, 5Department of Computer Science, Yale University, New Haven, CT and 6Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joel","family":"Rozowsky","sequence":"additional","affiliation":[{"name":"1 Program in Computational Biology and Bioinformatics, 2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 3Wyss Institute for Biologically-Inspired Engineering at Harvard, Boston, MA, 4Department of Genetics, Harvard Medical School, Boston, MA, 5Department of Computer Science, Yale University, New Haven, CT and 6Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ashish","family":"Agarwal","sequence":"additional","affiliation":[{"name":"1 Program in Computational Biology and Bioinformatics, 2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 3Wyss Institute for Biologically-Inspired Engineering at Harvard, Boston, MA, 4Department of Genetics, Harvard Medical School, Boston, MA, 5Department of Computer Science, Yale University, New Haven, CT and 6Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA"},{"name":"1 Program in Computational Biology and Bioinformatics, 2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 3Wyss Institute for Biologically-Inspired Engineering at Harvard, Boston, MA, 4Department of Genetics, Harvard Medical School, Boston, MA, 5Department of Computer Science, Yale University, New Haven, CT and 6Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Snyder","sequence":"additional","affiliation":[{"name":"1 Program in Computational Biology and Bioinformatics, 2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 3Wyss Institute for Biologically-Inspired Engineering at Harvard, Boston, MA, 4Department of Genetics, Harvard Medical School, Boston, MA, 5Department of Computer Science, Yale University, New Haven, CT and 6Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark","family":"Gerstein","sequence":"additional","affiliation":[{"name":"1 Program in Computational Biology and Bioinformatics, 2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 3Wyss Institute for Biologically-Inspired Engineering at Harvard, Boston, MA, 4Department of Genetics, Harvard Medical School, Boston, MA, 5Department of Computer Science, Yale University, New Haven, CT and 6Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA"},{"name":"1 Program in Computational Biology and Bioinformatics, 2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 3Wyss Institute for Biologically-Inspired Engineering at Harvard, 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