Re: [galaxy-user] Annotation

2012-04-04 Thread Jennifer Jackson
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

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

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
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

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