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Question: Software Post Alignment
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gravatar for Ianiri, Giuseppe
5.7 years ago by
Ianiri, Giuseppe • 90
Ianiri, Giuseppe • 90 wrote:
Hello, I performed my mapping using tophat - cufflink - cuffmerge - cuffdiff. With the information I have for my analysis so far, I can reannotate wrong genes, check for correct splicing etc. However, I would like to perform some analysis post-alignment, like for example samples clustering, volcano plot, heat maps etc. I guess I can't do this kind of analysis with Galaxy (I am using the free version on line on my Windows laptop) since I haven't found anything in the tools section. Does anyone know a software that I could use in windows with the data obtained in Galaxy? Any suggestion is really appreciated. Regards, Giuseppe Giuseppe Ianiri, Ph.D. Division of Cell Biology and Biophysics School of Biological Sciences 5100 Rockhill Road University of Missouri-Kansas City Kansas City, MO 64110 Email: ianirig@umkc.edu
rna-seq cuffmerge • 709 views
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modified 5.7 years ago by Jeremy Goecks • 2.2k • written 5.7 years ago by Ianiri, Giuseppe • 90
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gravatar for Jeremy Goecks
5.7 years ago by
Jeremy Goecks • 2.2k
Jeremy Goecks • 2.2k wrote:
Hi Giuseppe, You're probably looking for something like Cummerbund: http://compbio.mit.edu/cummeRbund/ which has a wrapper in the tool shed: http://toolshed.g2.bx.psu.edu/view/jjohnson/cummerbund This isn't on our public server yet, but it may be added in the future. You might look into using Galaxy Cloud, where you can add tools to your instance: http://wiki.galaxyproject.org/CloudMan Good luck, J.
ADD COMMENT • link written 5.7 years ago by Jeremy Goecks • 2.2k
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