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 Post subject: GREAT for RNA-seq?
PostPosted: Sun Jul 14, 2013 3:10 am 
Hi,
Thanks for the GREAT tool (especially for the option to use it with zebrafish). Even though it looks like GREAT was originally designed for GO analysis of non-coding regions, I was wondering whether it would be possible to use GREAT to calculate GO enrichment of RNA-seq data (i.e differentially expressed genes). For example, if I would paste the BED file of transcripts upregulated in one condition, would the GO enrichments that I obtain still be correct?
Thanks,
Ozren
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PostPosted: Thu Jul 18, 2013 11:38 am 
Site Admin
Hi,

You can indeed use GREAT to analyze your RNA-seq data. A similar question was asked at viewtopic.php?f=2&t=990 and the answer outlines how you can go about your analysis.

I would also consider using the foreground/background feature of GREAT. Also make sure you map your transcripts to the TSSs of those used by GREAT (http://bejerano.stanford.edu/help/display/GREAT/Genes).

Thanks,
Bejerano Team
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PostPosted: Wed Jul 24, 2013 10:43 pm 
Thanks!
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