I have to say that's a very nice visualization. Well done.
Jim
On Apr 20, 2011, at 9:28 PM, Jeremy Goecks wrote:
Vasu,
Here are the steps to create this visualization; this is relatively
new functionality, and you'll want to use our test server ( http://test.g2.bx.psu.edu/
) for now.
(1) Create a new visualization from the main menu: Visualization -->
New Track Browser and choose your genome build.
(2) Add your Cufflinks GTF files to the visualization using the 'Add
Tracks' button in the upper right of the visualization. (Adding the
Tophat reads and/or annotation tracks might prove useful as well.)
(3) Zoom in (use the button at the top, double click on a point, or
drag to select an area on the genome coordinates at the top) until
the track's menu has the option 'Show filters' and choose this
option to show filters.
(4) Once filters are visible, you should be able to drag the slider
to dynamically filter transcripts.
Here's an example visualization of some mapped Tophat reads and
Cufflinks transcripts that you can try out:
http://test.g2.bx.psu.edu/u/jeremy.goecks/v/assembly-of-h1-hesc-rna-seq-data
We're continuing to refine and extend this functionality and the
Galaxy Track Browser in general; questions/comments/suggestions are
most welcome.
Best,
J.
On Apr 19, 2011, at 9:28 AM, vasu punj wrote:
Thanks Jeremy,
This appear to be a useful function. Could you please enlist the
steps in workflow to achieve the above visualization or
alternatively point me to the URL where it is summarized please. I
believe it will take Tophat out put Bam file and fpkm tracking
file. I tried but I dont see track browser unless i convert to
GTF file format. Further if you can point me how to get the slider
window function as shown in snap shot that will be great. Good
work Jeremy!
Thanks.
Vasu
--- On Sun, 4/17/11, Jeremy Goecks <[email protected]> wrote:
From: Jeremy Goecks <[email protected]>
Subject: Re: Normalization an dplotting of RPKM/FPKM after cufflink
To: "vasu punj" <[email protected]>
Cc: [email protected]
Date: Sunday, April 17, 2011, 3:45 PM
Vasu,
> I want to include the following discussion in my message
regarding use Bam files of Tophat to visualize reads either in IGV
or Galaxy or other tools.
> I want to find out if I can plot RPKM/FPKM normalized values
> after running differential analysis in Cufflinks.
Galaxy has a number of tools for analyzing numerical data; look
under the menu items Statistics and Graph/Display Data for useful
tools. If you're looking to plot FPKM values in addition to mapped
reads from Tophat and Cufflinks transcripts, the Galaxy Tracks
Browser might prove useful as it has filtering functionality so
that you can move a slider to show/hide data based on FPKM values;
its often useful to use the sliders for FPKM measures to get a
sense of your data. See the attached screenshot for an example.
Best,
J.
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___________________________________________________________
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/
