CisGenome Issue

[Nicholas_]

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.
Thnx
Nick