Your message dated Tue, 29 Sep 2015 22:00:13 +0000
with message-id <e1zh2wx-0000ti...@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.
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--
778589: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=778589
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: wnpp
Severity: wishlist
Owner: Debian Med team <debian-...@lists.debian.org>
X-Debbugs-Cc: debian-de...@lists.debian.org, debian-...@lists.debian.org
* Package name : express
Version : 1.5.1
Upstream Author : Adam Roberts & Lior Pachter <ask.x...@gmail.com>
* URL : http://bio.math.berkeley.edu/eXpress/index.html
* License : Artistic-2.0
Programming Lang: C++
Description : Streaming quantification for high-throughput sequencing
eXpress is a streaming tool for quantifying the abundances of a set of
target sequences from sampled subsequences. Example applications include
transcript-level RNA-Seq quantification, allele-specific/haplotype
expression analysis (from RNA-Seq), transcription factor binding
quantification in ChIP-Seq, and analysis of metagenomic data. It is
based on an online-EM algorithm that results in space (memory)
requirements proportional to the total size of the target sequences and
time requirements that are proportional to the number of sampled
fragments. Thus, in applications such as RNA-Seq, eXpress can accurately
quantify much larger samples than other currently available tools
greatly reducing computing infrastructure requirements. eXpress can be
used to build lightweight high-throughput sequencing processing
pipelines when coupled with a streaming aligner (such as Bowtie), as
output can be piped directly into eXpress, effectively eliminating the
need to store read alignments in memory or on disk.
.
In an analysis of
the performance of eXpress for RNA-Seq data, we have observed that this
efficiency does not come at a cost of accuracy. eXpress is more accurate
than other available tools, even when limited to smaller datasets that
do not require such efficiency. Moreover, like the Cufflinks program,
eXpress can be used to estimate transcript abundances in multi-isoform
genes. eXpress is also able to resolve multi-mappings of reads across
gene families, and does not require a reference genome so that it can be
used in conjunction with de novo assemblers such as Trinity, Oases, or
Trans-ABySS. The underlying model is based on previously described
probabilistic models developed for RNA-Seq but is applicable to other
settings where target sequences are sampled, and includes parameters for
fragment length distributions, errors in reads, and sequence-specific
fragment bias.
.
eXpress can be used to resolve ambiguous mappings in other
high-throughput sequencing based applications. The only required inputs
to eXpress are a set of target sequences and a set of sequenced
fragments multiply-aligned to them. While these target sequences will
often be gene isoforms, they need not be. Haplotypes can be used as the
reference for allele-specific expression analysis, binding regions for
ChIP-Seq, or target genomes in metagenomics experiments. eXpress is
useful in any analysis where reads multi-map to sequences that differ in
abundance.
Express is a dependency of trinityrnaseq. The Debian Med team will be group
maintaining it.
--- End Message ---
--- Begin Message ---
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 778...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Michael R. Crusoe <cru...@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 ftpmas...@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-packag...@lists.alioth.debian.org>
Changed-By: Michael R. Crusoe <cru...@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)
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