taller so it will be easier to see?
>
> Thanks,
>
>
> tao
>
> -Original Message-
> From: Jennifer Jackson [mailto:j...@bx.psu.edu]
> Sent: Tuesday, September 27, 2011 1:13 PM
> To: Peng, Tao
> Cc: galaxy-user
> Subject: Re: [galaxy-user] run tophat in
/transcript expression from Cuffdiff
results.
Thanks,
tao
-Original Message-
From: Peng, Tao
Sent: Friday, September 30, 2011 3:13 PM
To: 'Jennifer Jackson'
Cc: galaxy-user
Subject: RE: [galaxy-user] run tophat in galaxy
Thanks a lot.
Please see the attached screen shot
[mailto:j...@bx.psu.edu]
Sent: Tuesday, September 27, 2011 1:13 PM
To: Peng, Tao
Cc: galaxy-user
Subject: Re: [galaxy-user] run tophat in galaxy
Hi Tao,
Yes, the resulting SAM dataset can be converted to BAM and viewed in the
GTB (Galaxy Track Browser).
http://galaxyproject.org/wiki/Learn -> scroll
PM
To: galaxy-user
Cc: Peng, Tao
Subject: Re: [galaxy-user] run tophat in galaxy
===> Please use "Reply All" when responding to this email! <===
Hi Tao,
I made an error in my prior reply, it is possible to guide assembly in
TopHat. To do this, on the TopHat form, change "T
r Jackson [mailto:j...@bx.psu.edu]
Sent: Thursday, September 15, 2011 2:37 PM
To: galaxy-user
Cc: Peng, Tao
Subject: Re: [galaxy-user] run tophat in galaxy
===> Please use "Reply All" when responding to this email!<===
Hi Tao,
I made an error in my prior reply, it is possible to gu
===> Please use "Reply All" when responding to this email! <===
Hello,
Chromosome names will need to be modified once the file is imported, as
explained in #5 of the FAQ:
http://usegalaxy.org/u/jeremy/p/transcriptome-analysis-faq
Hopefully this helps,
Best,
Jen
Galaxy team
On 9/15/11 8:22
I have related question If I have to use Ensembl mouse GTF file
(Mus_musculus.NCBIM37.64) Do I have to download and reformat it or Galaxy
can take it from the source directly?
Thanks
On Sun, Aug 28, 2011 at 8:50 AM, Peng, Tao wrote:
> ===> Please use "Reply All" when responding to this email!
===> Please use "Reply All" when responding to this email! <===
Hi Tao,
I made an error in my prior reply, it is possible to guide assembly in
TopHat. To do this, on the TopHat form, change "TopHat settings to use:"
from "Use Defaults" to "Full parameter list". In the expanded form:
1 - chan
===> Please use "Reply All" when responding to this email! <===
Hello Tao,
Sorry for the delayed reply, your question did not post to the mailing
list since the "to" was not _only_ to galaxy-user.
Going forward, please leave off any "to" or "cc" to team members when
asking a question. Send a
===> Please use "Reply All" when responding to this email! <===
Hi how can I specify a GTF gene annotation file when running tophat to guide
the alignment to human genome? What is the best way to visualize the tophat
results in the context of annotated human genome, i.e. RefSeq?
Thanks,
tao
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