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Old 05-28-2014, 09:21 AM   #1
Parharn
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Default Gene enrichment on cuffdiff output

Hi every body,
I have mapped my seqs with Toxedo pipeline and have my diff_out file out of cuffdiff. Now I want to do some gene enrichment analysis on it. I need some help on what to do and how to do. A bit of more detailed help since it is my first time. Any more information you need please let me know.

Thanks,
Parham
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Old 10-27-2014, 06:40 PM   #2
Roger Z
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Quote:
Originally Posted by Parharn View Post
Hi every body,
I have mapped my seqs with Toxedo pipeline and have my diff_out file out of cuffdiff. Now I want to do some gene enrichment analysis on it. I need some help on what to do and how to do. A bit of more detailed help since it is my first time. Any more information you need please let me know.

Thanks,
Parham

Hi,Parharn,have you solved the problem?
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Old 10-28-2014, 02:00 AM   #3
Parharn
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Hi Roger, Yes I managed to do some GO enrichment analysis and pathway analysis on it! Thanks for asking. Do you suggest anything else?
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Old 10-28-2014, 02:05 AM   #4
Roger Z
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Originally Posted by Parharn View Post
Hi Roger, Yes I managed to do some GO enrichment analysis and pathway analysis on it! Thanks for asking. Do you suggest anything else?
Hi,Parham. I am also using cufflinks output to do GO and kegg pathway enrichment analysis, but I encounter with some difficulties. You can see it here:
http://seqanswers.com/forums/showthread.php?t=47806

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