Previous topic | Next topic
Author Message
 Post subject: GREAT for snp enrichment
PostPosted: Thu Jun 06, 2013 3:55 am 
Hello,

Thanks for the great tool. I'm doing enrichment for snp data generated by exome sequencing (convert to .bed and analyze). However, I was not able to use the exome capture regions as the background so I used the whole genome as background. Can I still use the results somehow or is there a way to make statistically solid interpretation for this kind of input data?

br,
Tommi
Report this post   
Reply with quote  
 
 Post subject:
PostPosted: Thu Jul 18, 2013 9:31 am 
Site Admin
Tommi,

I would suggest converting all genes sequenced to their canonical TSS using the gene set at http://bejerano.stanford.edu/help/display/GREAT/Genes/. If one of your genes is not present in the gene set, it it is because it is not annotated for function in GO.

Then, I would submit this full set using GREAT's "Background regions" section and then set of TSSs that contain a SNP as "Test regions". This will give you results that use a region-based foreground background hypergeometric statistic (http://bejerano.stanford.edu/help/display/GREAT/Statistics). It is not the same as the region based binomial test used by the full genome analysis, but currently GREAT does not support the ability to redefine the background genome.

Additionally, I would suggest playing with the parameters when using the foreground/background feature of GREAT since various background sets require different optimization of thresholds such as minimum fold.

Thanks,
Bejerano Team
Report this post   
Reply with quote  
 
Post New Topic » Reply »  Page 1 of 1   [ 2 posts ]  



Who is online

Users browsing this forum: No registered users and 1 guest


You cannot post new topics in this forum
You cannot reply to topics in this forum
You cannot edit your posts in this forum
You cannot delete your posts in this forum

Search for:
Jump to:  
cron
Fatal: Not able to open ./cache/data_global.php