Hello,
The tools TopHat/Cufflinks will map and assemble transcripts from
sequencing reads. This mapping give each component (short read,
transcript, gene boundary) genomic coordinates with respect to the
target reference genome.
Annotation is also mapped to the reference genome by genomic
Subject: Re: [galaxy-user] annotation file for cufflinks
I had a similar question, after i downloaded a bacterial ref genome GFF file
and loaded it into Galaxy, the use reference annotation feature of Cufflinks
kept telling it need to be the GTF file instead,
When I check the Cufflinks manual at http
I had a similar question, after i downloaded a bacterial ref genome
GFF file and loaded it into Galaxy, the use reference annotation
feature of Cufflinks kept telling it need to be the GTF file instead,
When I check the Cufflinks manual at http://cufflinks.cbcb.umd.edu/manual.html
It looks
If using Ensembl make sure it is properly formatted.
Vasu
--- On Tue, 8/30/11, Peng, Tao tp...@fhcrc.org wrote:
From: Peng, Tao tp...@fhcrc.org
Subject: [galaxy-user] annotation file for cufflinks
To: Jennifer Jackson j...@bx.psu.edu, galaxy-user
galaxy-user@lists.bx.psu.edu
Date: Tuesday,
UCSC should work fine.
Vasu
--- On Tue, 8/30/11, Peng, Tao tp...@fhcrc.org wrote:
From: Peng, Tao tp...@fhcrc.org
Subject: RE: [galaxy-user] annotation file for cufflinks
To: vasu punj pu...@yahoo.com, Jennifer Jackson j...@bx.psu.edu,
galaxy-user galaxy-user@lists.bx.psu.edu
Date: Tuesday
In the cufflink site, they have annotation from ucsc,ncbi ensemble. not sure
which one to download and then load into galaxy?
thanks,
Tao
Sent from my iPhone
On Aug 30, 2011, at 5:52 PM, vasu punj pu...@yahoo.com wrote:
If using Ensembl make sure it is properly formatted.
Vasu
--- On
; Peng, Tao
Subject: Re: [galaxy-user] annotation file for cufflinks
If using Ensembl make sure it is properly formatted.
Vasu
--- On Tue, 8/30/11, Peng, Tao tp...@fhcrc.org wrote:
From: Peng, Tao tp...@fhcrc.org
Subject: [galaxy-user] annotation file for cufflinks
To: Jennifer Jackson j
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