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 a column labeled as "name2" (as defined in the extended genePred
format at UCSC and which is not included in BED or GTF format output
file types).
As the other users have pointed out, a valid GTF file format for the
Cuff* programs to use is the goal. Currently, some manipulation of the
available reference files from many of the common sources is necessary
to get the formatting correct. The Galaxy team is aware of the issues
with external files concerning format and is working on potential solutions.
Thank you for your patience while we work out the kinks with the newly
added tool suite,
Best,
Jen
Galaxy team
On 1/24/11 7:02 AM, Jeremy Goecks wrote:
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 from UCSC; when you
are getting the file, you'll want to select the table with the word
'canonical' in it. E.g. for hg19/UCSC genes, there is a table called
knownCanonical that provides the canonical gene names.
Thanks,
J.
On Jan 24, 2011, at 9:38 AM, vasu punj wrote:
This is a knwon issue of GTF file from Ensembl
--- On *Mon, 1/24/11, Matteo Bovolenta /<[email protected]
<mailto:[email protected]>>/* wrote:
From: Matteo Bovolenta <[email protected] <mailto:[email protected]>>
Subject: [galaxy-user] Gene Name in Cufflink/compare/diff
To: [email protected] <mailto:[email protected]>
Date: Monday, January 24, 2011, 5:05 AM
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?
Thank you all very much for the support,
Best Regards,
Matteo
--
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Dipartimento di Medicina Sperimentale e Diagnostica
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