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! 
--- On Sun, 4/17/11, Jeremy Goecks <> wrote:

From: Jeremy Goecks <>
Subject: Re: Normalization an dplotting of RPKM/FPKM after cufflink
To: "vasu punj" <>
Date: Sunday, April 17, 2011, 3:45 PM


> 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.

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