___
From: galaxy-user-boun...@lists.bx.psu.edu
[galaxy-user-boun...@lists.bx.psu.edu] on behalf of Du, Jianguang
[jia...@iupui.edu]
Sent: Thursday, August 23, 2012 4:01 PM
To: Jennifer Jackson
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galax
...@lists.bx.psu.edu
[galaxy-user-boun...@lists.bx.psu.edu] on behalf of Du, Jianguang
[jia...@iupui.edu]
Sent: Thursday, August 23, 2012 4:01 PM
To: Jennifer Jackson
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] Should I use iGenomes verson of a reference GTF for
Tophat?
Hi Jen,
Than
t; From: Jennifer Jackson [j...@bx.psu.edu]
> Sent: Thursday, August 23, 2012 11:46 AM
> To: Du, Jianguang
> Cc: galaxy-user@lists.bx.psu.edu
> Subject: Re: [galaxy-user] Should I use iGenomes verson of a reference GTF
> for Tophat?
>
> Hello Jianguang,
>
> When in the analy
s.bx.psu.edu
Subject: Re: [galaxy-user] Should I use iGenomes verson of a reference GTF for
Tophat?
Hello Jianguang,
When in the analysis process to start using the reference GTF file can
depend on whether or not you intend to do any discovery along with
differential expression testing. At the
ms/splicing?
Thanks.
Jianguang
From: Jennifer Jackson [j...@bx.psu.edu]
Sent: Thursday, August 23, 2012 11:46 AM
To: Du, Jianguang
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] Should I use iGenomes verson of a reference GTF for
Tophat?
Hello Jia
Hello Jianguang,
When in the analysis process to start using the reference GTF file can
depend on whether or not you intend to do any discovery along with
differential expression testing. At the TopHat and Cufflinks steps,
using reference GTF file can influence how datasets will map and
assem
Dear All,
I am analysing RNA-seq datasets for differential splicing events between cell
types. These are mouse cells. Jen suggested me to use the iGenomes version of
reference GTF to take full advantage of the options in CuffDiff. My question
is: should I use this iGenome version reference GTF
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