Re: [galaxy-user] annotation file for cufflinks

2011-09-24 Thread Jiannong Xu
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

Re: [galaxy-user] annotation file for cufflinks

2011-09-23 Thread Gary Xie
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

[galaxy-user] annotation file for cufflinks

2011-08-30 Thread Peng, Tao
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

Re: [galaxy-user] annotation file for cufflinks

2011-08-30 Thread vasu punj
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

Re: [galaxy-user] annotation file for cufflinks

2011-08-30 Thread vasu punj
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

Re: [galaxy-user] annotation file for cufflinks

2011-08-30 Thread Peng, Tao
, 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, August 30, 2011, 1:52 PM Hi jen and galaxy users, when I try

Re: [galaxy-user] annotation file for cufflinks

2011-08-30 Thread Peng, Tao
; 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