Hi Bernardo,
> Hello Galaxy community,
>
>
> I would like to know if there is any available tool in Galaxy for
> automated gene annotation. I need gene annotation in GTF or GFF3
> format to run CuffDiff on a RNA-Seq project that we are.
We have a tool, that annotates your prokaryotic genome, th
Hello Galaxy community,
I would like to know if there is any available tool in Galaxy for automated
gene annotation. I need gene annotation in GTF or GFF3 format to run
CuffDiff on a RNA-Seq project that we are.
If not, do you recommend me any software or utility. We have the genome
annotated in G
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
c
Dear galaxy users,
This might be a very basic question to most of you. But I was hopimg I could
get better understanding of this concept by asking you all.
How exactly can we accomplish annotation of our reads? The combination of
Tophat and cufflinks does annotate genes right? . I am a bit confus
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 manu
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 l
; 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 wrote:
From: Peng, Tao
Subject: [galaxy-user] annotation file for cufflinks
To: "Jennifer Jackson" , "galaxy-user"
D
gt;
> --- On Tue, 8/30/11, Peng, Tao wrote:
>
> From: Peng, Tao
> Subject: [galaxy-user] annotation file for cufflinks
> To: "Jennifer Jackson" , "galaxy-user"
>
> Date: Tuesday, August 30, 2011, 1:52 PM
>
> Hi jen and galaxy users, when I try to
UCSC should work fine.
Vasu
--- On Tue, 8/30/11, Peng, Tao wrote:
From: Peng, Tao
Subject: RE: [galaxy-user] annotation file for cufflinks
To: "vasu punj" , "Jennifer Jackson" ,
"galaxy-user"
Date: Tuesday, August 30, 2011, 10:53 PM
Hi I have down-loaded U
If using Ensembl make sure it is properly formatted.
Vasu
--- On Tue, 8/30/11, Peng, Tao wrote:
From: Peng, Tao
Subject: [galaxy-user] annotation file for cufflinks
To: "Jennifer Jackson" , "galaxy-user"
Date: Tuesday, August 30, 2011, 1:52 PM
Hi jen and galaxy user
Hi jen and galaxy users, when I try to use cufflinks in GALAXY and select "use
reference annotation", I am NOT sure how to get the annotation file in GTF
format for cufflinks.
I was trying to down-load the annotation file from Illumina donated package in
Cufflink website, I am NOT sure this is
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