(cc'ing galaxy-user)
Sorry Jeremy, I'm being a bit dense here - where exactly are these tools in
> the tool list - I can't find them...
David,
Both tools are located within the 'Operate on Genomic Intervals' menu. Also,
remember that tool search (Options -> Show Tool Search) is useful for
fin
;>
>> --- On Tue, 3/1/11, Ying Zhang wrote:
>>
>>
>> From: Ying Zhang
>> Subject: Re: [galaxy-user] how to find out the gene_ID correspond to CUFF ID
>> To: "David Matthews"
>> Cc: galaxy-u...@bx.psu.edu
>> Date: Tuesday, March 1, 20
find out the gene_ID correspond to CUFF ID
To: "David Matthews"
Cc: galaxy-u...@bx.psu.edu
Date: Tuesday, March 1, 2011, 10:59 AM
Dear David:
I followed your advices and downloaded reference sequence from
Emsemble, then I
uploaded this file into galaxy, and then I run the cufflinks
I believe you need to format the Ensemble file Chromosome columns is not
correct.
Vasu
--- On Tue, 3/1/11, Ying Zhang wrote:
From: Ying Zhang
Subject: Re: [galaxy-user] how to find out the gene_ID correspond to CUFF ID
To: "David Matthews"
Cc: galaxy-u...@bx.psu.edu
Date: Tuesda
Dear David:
I followed your advices and downloaded reference sequence from
Emsemble, then I
uploaded this file into galaxy, and then I run the cufflinks using the
file as a
reference annotation, however I got error when I am running, the following the
error message gave to me:
An error occur
Hi,
Yeah, thats a good idea too!! I did not know about that tool, shows what I know
(!) - thanks for the info!
Cheers
David
On 1 Mar 2011, at 04:51, Jeremy Goecks wrote:
> Ying, you could also try using the tools 'Fetch closest non-overlapping
> feature' and 'Intersect' to find genes nearby
Ying, you could also try using the tools 'Fetch closest non-overlapping
feature' and 'Intersect' to find genes nearby transcripts/genes/TSSes of
interest; for both tools, you'll want a reference annotation, either from UCSC
or Ensembl.
Best,
J.
On Feb 28, 2011, at 6:10 PM, David Matthews wrote
Hi,
You need to supply a gene annotation file with cufflink to easily get the
gene-id information. Without it, cufflinks simply tries its best to figure out
what genes are present. The ensemble gtf file is quite a comprehensive one -
there is a link to it on the cufflinks manual page.
Good luc
Dear Everyone:
I have got one output file after I run Cufflink which contain gene expression
information. However, I found out for each gene_ID, it has the format like,
CUFF.1151175, do you have idea of how to find out the offical gene ID
correspond to this CUFF ID? Thank you very much!
Best
Yin
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