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Old 10-10-2011, 01:24 AM   #1
Junior Member
Location: Athens

Join Date: Apr 2011
Posts: 2
Default CisGenome Issue

Hello all,

So i have been struggling a lot with the analysis of some data from ChIP-seq experiment.

I am a biologist, not a statistician, not an informatician.

I am using CisGenome for the analysis of my data. When i use the peak caller

with its default settings, the total number of peaks given is different than the

total number i get when i add categories of my own [i.e. peaks in promoters, gene deserts, gene bodies, upstream enhancers, downstream enhancers]

Can anybody tell me why is this happening? It is driving me mad and i can't figure it out. Maybe it's naive but i can't see it.

Note that when i add my categories of interest, i assign every peak to genes. So could that be it? One peak be assigned on different categories? [i.e. one peak could be assigned both on promoter of one gene and on the upstream enhancer of another gene?]

Any piece of advise would be greatly appreciated.
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