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 <jeremy.goecks@emory.edu> wrote:

From: Jeremy Goecks <jeremy.goecks@emory.edu>
Subject: Re: Normalization an dplotting of RPKM/FPKM after cufflink
To: "vasu punj" <punjv@yahoo.com>
Cc: galaxy-user@bx.psu.edu
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.