Hi all,
when I run a RNASeq analysis using tophat, cufflink, coffcompare and
cuffdiff by aligning my data to the RefSeq genes I obtain tables from
cufflink/compare/diff which does not include the gene name, but only
the NM_.
Does someone knows how I can obtain all the tables with the gene name?
T
We'd like to announce an update to Galaxy CloudMan - a completely standalone
version Galaxy on Amazon's cloud.
The new version has been released that brings a number of improvements to
the core functionality of CloudMan and expands the number of tools available
within Galaxy CloudMan to match that
Hello,
I have followed the steps described by Jeremy in his exercise
(http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise) to
analyze RNA-seq data and all of the steps seemed to go ok except that at the
end the gene IDs were missing, so for example the file CDS diff file had
n
Hello Sonali,
More API help can be found in the README and example scripts in the
source code location: galaxy-dist/scripts/api. We have plans to
incorporate more of this into the wiki soon, but for now, this is best
place to get API information.
Hopefully this helps,
Jen
Galaxy team
On 1/
Hello Slim,
Would you please share a link to your history (Options -> Share or
Publish) and I can take a look? You can email me directly with the link.
Best,
Jen
Galaxy team
On 1/24/11 5:47 AM, Slim Sassi wrote:
Hello,
I have followed the steps described by Jeremy in his exercise
(http://m
This is a knwon issue of GTF file from Ensembl
--- On Mon, 1/24/11, Matteo Bovolenta wrote:
From: Matteo Bovolenta
Subject: [galaxy-user] Gene Name in Cufflink/compare/diff
To: galaxy-u...@bx.psu.edu
Date: Monday, January 24, 2011, 5:05 AM
Hi all,
when I run a RNASeq analysis using tophat,
Hi Matteo and Vasu,
There are different ways to refer to genes. Names that start with NM_ are
termed 'accession numbers,' and they are a valid way to refer to genes.
Matteo, what you may want is the canonical gene name (e.g. Xkr4). If so, you'll
want to use a gene annotation/reference file fro
Hi,
What I am trying is,
A) to write an exec_after_process for tool1(Scatterer tool). This tool1
gives multiple outputs(in the form of files names generated by Galaxy).
--
Thanks Jeremy,
The issue mentioned by Slim is also related to the same issue as of Matteo. In
the end out put files either dont have geneIDS or has multiple enteries of
particular gene. Any suggestion?
--- On Mon, 1/24/11, Slim Sassi wrote:
From: Slim Sassi
Subject: [galaxy-user]
For the ensembl annotation, you can download the gtf file from ensembl for your
organism here:
http://uswest.ensembl.org/info/data/ftp/index.html
To use this, you need to fix it because the chromosome names are not correct
(depending on your organism, it is not correct for mouse and rat at leas
Hello Matteo,
The UCSC Genes table knownCanonical is one source for gene names, but
another choice would be the RefSeq Genes track's primary table
"refGene". When extracting from the UCSC Table browser, use the output
file type of "all fields from selected table". The gene name will be
under
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Thanks!
Jen
Galaxy team
On 1/24/11 8:01 AM, Ralf JAUCH wrote:
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