Re: [galaxy-user] Normalization and plotting of RPKM/FPKM after cufflink
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.
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 <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.
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 <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.
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participants (3)
-
Jeremy Goecks -
Jim Robinson -
vasu punj