Thanks a lot.
Please see the attached screen shot from using Browser in GALAXY for
viewing results of Tophat. What do those numbers mean? Is there any way
to adjust Y-axis to have the bar 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 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 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
>>
>>
>> ___________________________________________________________
>> 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

___________________________________________________________
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