Jen, thank you for following up on my question.
Is any tool in GALAXY to visualize the coverage of aligned reads from
TopHat on human chromosomes (histogram or density plot)?

Tao

-----Original Message-----
From: Jennifer 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 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 - change "Use Own Junctions:" to be "yes".
2 - change "Use Gene Annotation Model:" to be "yes"
3 - in the new pull-down menu, select the GTF file from your history

Great question! Glad that we were able to provide you with the correct 
instruction,

Best,

Jen
Galaxy team

On 9/15/11 1:38 PM, Jennifer Jackson wrote:
> ===> 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 all questions directly "to"
> "galaxy-u...@bx.psu.edu" and do not include any "Re" or "Fwd" text in
> the subject line.
>
> Regarding RNA-seq analysis and reference GTF files, the place to
> incorporate the GTF file is in the Cufflinks step, the option to
select
> the GTF file from your history is on the tool's form. If you have
> questions about the tools that are not addressed by these help links:
>
> http://usegalaxy.org/u/jeremy/p/transcriptome-analysis-faq
> http://usegalaxy.org/u/jeremy/p/galaxy-rna-seq-analysis-exercise
>
> then contacting the tool authors would be the next step:
> email tophat.cuffli...@gmail.com
>
> To visualize the data, the available options will be links associated
> with each dataset (expand the dataset box to locate these). The Galaxy
> Track Browser (GTB) aka "Trackster", UCSC Genome Browser, Ensembl, and
> GeneTrack are potential options; the datatype will determine which
links
> are provided.
>
> Hopefully this helps,
>
> Best,
>
> Jen
> Galaxy team
>
>
> -------- Original Message --------
> Subject: run tophat in galaxy
> Date: Sun, 28 Aug 2011 08:50:04 -0700
> From: Peng, Tao <tp...@fhcrc.org>
> To: Jennifer Jackson <j...@bx.psu.edu>, galaxy-user
> <galaxy-user@lists.bx.psu.edu>
>
>
>
> 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
>
>
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org. Please keep all replies on the list by
> using "reply all" in your mail client. For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
> http://lists.bx.psu.edu/

-- 
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to