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 to "Visualization" to find:
http://galaxyproject.org/wiki/Learn/Visualization

The GTB can be reached through a different links, but one quick way to do this is:

1 - start with TopHat's output SAM dataset
2 - use the tool "NGS: SAM Tools -> SAM-to-BAM"
3 - hover over "Visualization" in the top menu bar then click on "New Track Browser" 4 - at the prompt, name the visualization and specify the reference genome and click on "Continue" 5 - once the browser opens, click on the "Add Datasets to Visualization" prompt to add datasets. Histories and Libraries can be navigated, selected, then individual datasets selected and loaded.
6 - default view for BAM datasets a coverage histogram.
7 - adding more tracks and other functions can be performed by using the left menu "Actions" on the GTB interface. Be sure to use "Save" before navigating away if you want to use the same browser again.

If datasets are not available to add to a browser, then likely there is a mismatch between the browser's reference database and the database assigned to the dataset. In some cases this can and should be adjusted (perhaps database was unassigned after an analysis).

The SAM file can also be converted to interval, then BED format for visualization, but BAM is the most direct route and preserves the sequence content when zoomed in at the base level.

Hopefully this helps you and others to learn more about the GTB. This tool is under active development. Screencasts and more example documentation is on the way soon to offer more help.

Best,

Jen
Galaxy team

On 9/27/11 12:45 PM, Peng, Tao wrote:
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


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--
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http://usegalaxy.org
http://galaxyproject.org/Support
___________________________________________________________
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Galaxy analysis and other features on the public server
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