Your message dated Tue, 29 Sep 2015 22:00:13 +0000 with message-id <E1Zh2wX-0000TI-8b@franck.debian.org> and subject line Bug#778589: fixed in berkeley-express 1.5.1-1 has caused the Debian Bug report #778589, regarding "ITP: berkeley-express -- Streaming quantification for high to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact owner@bugs.debian.org immediately.) -- 778589: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=778589 Debian Bug Tracking System Contact owner@bugs.debian.org with problems
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- To: Debian Bug Tracking System <submit@bugs.debian.org>
- Subject: ITP: express -- Streaming quantification for high-throughput sequencing
- From: Michael Crusoe <michael.crusoe@gmail.com>
- Date: Tue, 17 Feb 2015 03:07:54 +0000
- Message-id: <CAD=Wrc+MVGCOwEspKv_Z5UAf4yA7qeAJR9ndwhrQL1S0s0_BJA@mail.gmail.com>
Package: wnppSeverity: wishlistOwner: Debian Med team <debian-med@lists.debian.org>X-Debbugs-Cc: debian-devel@lists.debian.org, debian-med@lists.debian.org* Package name : expressVersion : 1.5.1Upstream Author : Adam Roberts & Lior Pachter <ask.xprs@gmail.com>* License : Artistic-2.0Programming Lang: C++Description : Streaming quantification for high-throughput sequencingeXpress is a streaming tool for quantifying the abundances of a set oftarget sequences from sampled subsequences. Example applications includetranscript-level RNA-Seq quantification, allele-specific/haplotype_expression_ analysis (from RNA-Seq), transcription factor bindingquantification in ChIP-Seq, and analysis of metagenomic data. It isbased on an online-EM algorithm that results in space (memory)requirements proportional to the total size of the target sequences andtime requirements that are proportional to the number of sampledfragments. Thus, in applications such as RNA-Seq, eXpress can accuratelyquantify much larger samples than other currently available toolsgreatly reducing computing infrastructure requirements. eXpress can beused to build lightweight high-throughput sequencing processingpipelines when coupled with a streaming aligner (such as Bowtie), asoutput can be piped directly into eXpress, effectively eliminating theneed to store read alignments in memory or on disk..In an analysis ofthe performance of eXpress for RNA-Seq data, we have observed that thisefficiency does not come at a cost of accuracy. eXpress is more accuratethan other available tools, even when limited to smaller datasets thatdo not require such efficiency. Moreover, like the Cufflinks program,eXpress can be used to estimate transcript abundances in multi-isoformgenes. eXpress is also able to resolve multi-mappings of reads acrossgene families, and does not require a reference genome so that it can beused in conjunction with de novo assemblers such as Trinity, Oases, orTrans-ABySS. The underlying model is based on previously describedprobabilistic models developed for RNA-Seq but is applicable to othersettings where target sequences are sampled, and includes parameters forfragment length distributions, errors in reads, and sequence-specificfragment bias..eXpress can be used to resolve ambiguous mappings in otherhigh-throughput sequencing based applications. The only required inputsto eXpress are a set of target sequences and a set of sequencedfragments multiply-aligned to them. While these target sequences willoften be gene isoforms, they need not be. Haplotypes can be used as thereference for allele-specific _expression_ analysis, binding regions forChIP-Seq, or target genomes in metagenomics experiments. eXpress isuseful in any analysis where reads multi-map to sequences that differ inabundance.Express is a dependency of trinityrnaseq. The Debian Med team will be groupmaintaining it.
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- To: 778589-close@bugs.debian.org
- Subject: Bug#778589: fixed in berkeley-express 1.5.1-1
- From: crusoe@ucdavis.edu (Michael R. Crusoe)
- Date: Tue, 29 Sep 2015 22:00:13 +0000
- Message-id: <E1Zh2wX-0000TI-8b@franck.debian.org>
Source: berkeley-express Source-Version: 1.5.1-1 We believe that the bug you reported is fixed in the latest version of berkeley-express, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 778589@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Michael R. Crusoe <crusoe@ucdavis.edu> (supplier of updated berkeley-express package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmaster@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Fri, 21 Aug 2015 17:18:15 -0700 Source: berkeley-express Binary: berkeley-express berkeley-express-doc Architecture: source all amd64 Version: 1.5.1-1 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <crusoe@ucdavis.edu> Description: berkeley-express - Streaming quantification for high-throughput sequencing berkeley-express-doc - Documentation for RNA-Seq tool eXpress Closes: 778589 Changes: berkeley-express (1.5.1-1) unstable; urgency=low . * Initial release (Closes: #778589) Checksums-Sha1: 8f18ef2ffc5bdbb9edc3adfb36bcdf09d282de2e 2341 berkeley-express_1.5.1-1.dsc 173f5b340f69d50096271a0199716d0acbbaf446 931166 berkeley-express_1.5.1.orig.tar.gz a442720702535a59cb129f7d1c010f0637ba7f85 6684 berkeley-express_1.5.1-1.debian.tar.xz 670c8c46b93d55f9bacda5a0b739bf751282de74 790178 berkeley-express-doc_1.5.1-1_all.deb ab8c0f269378f074ef65fe12f786414270cfed85 634446 berkeley-express_1.5.1-1_amd64.deb Checksums-Sha256: e8e9e0b48eb40623f147a184fedaec9057539c55e395405b5244dfe9144b7b06 2341 berkeley-express_1.5.1-1.dsc 0c5840a42da830fd8701dda8eef13f4792248bab4e56d665a0e2ca075aff2c0f 931166 berkeley-express_1.5.1.orig.tar.gz f027b347e2d0141d7a37ab54fcac0af9de0ad9f1fb8c93278f62a65b741a4399 6684 berkeley-express_1.5.1-1.debian.tar.xz 63e81f3cb383d4823bdf5869d8eebfbf82e8595ff41e5cdfc17b8b41199d331d 790178 berkeley-express-doc_1.5.1-1_all.deb 3b91bdb8fb621dadf7185b21556a7b75cbced87b3c3b6056767addaec915856d 634446 berkeley-express_1.5.1-1_amd64.deb Files: 98d44704091553ea033b289bfba876bc 2341 science optional berkeley-express_1.5.1-1.dsc 525f99d4716291542c832c2b77310a75 931166 science optional berkeley-express_1.5.1.orig.tar.gz ca474e15a183a917373a28d3fb85f330 6684 science optional berkeley-express_1.5.1-1.debian.tar.xz d4abec264cb1bfe77138956894c10134 790178 doc optional berkeley-express-doc_1.5.1-1_all.deb 499d38578c9baf68b5ea46ebc8f6a96b 634446 science optional berkeley-express_1.5.1-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJV3rLoAAoJEFeKBJTRxkbRa+sQAIBK+0qBDuwJ3yv1/mDb6XSk 6PCNuWDONu6v8VnJXNja/44I/HcBGic/P8nO3VMtLJPWXHp5s27I/mninK4fbL8k nUzFIRbJoyD1effPge5Dspke5l8xlUbBYad03pqT2EesqHDOCSCY1W225sIviY99 4WxxMOXkYUoeprjsiYmpVOzFeJas/Xjh9CbxwW2vc1Fmf0Z5+Hnz7Y+GxWxoKuuN SQbZpQKhstQUJXJoU87u2gNvyGggOvLR8lCFctI5aZBHNkZm6F6HI94E1jSBR3+h z3yUUl62An+0T+AV2ucN9LCI1wQuGSvPO7w4oYHLvQLMnfmeLJjv6m4pcDvas8k/ 2IiZ4FeriqewODfsWkeS854410W0YZcH4XMj22pnVSkboHMw5Z8okOpa7MnFmDxz uNjYlRoXnkCKPNMZB36G0/Jc80LaYwKL+ZiieagOoptjz9qldkHYbrfGxSSyYGUY gOBpNp30FX7kDhaylWfIHfBj2IYt4LYnMWjDT9o8Sz9EtuuSQUim26B2wGmQ+E7w T/IRAMAiv7ngoy+8NrqUTXE8yESQJlH59y1Wu8btMJK1bHGbYZqTk/js6xRai2dA DNoDMVt0/7uT8EjMCRGurZGvuw/+tpalHWmyXi8wRvPwLCJsMUeSqJVQapDLATTQ I2ht1G0tnAok1gPpfHFZ =IyL1 -----END PGP SIGNATURE-----
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