[Bioc-sig-seq] general quesion regarding chipseq

[Tobias Straub]

dear all

i am doing my first steps into chipseq and have a few conceptual  
questions regarding the data treatment:

as a chipchip person i am used to work on ip/input ratios as numerical  
surrogate of biological binding. now i am about to analyze my first  
solexa datasets (have both ip and input material sequenced) and it  
appears as if the data needs ratio calculation as well as the input  
has quite some -probably copy dependent- heterogeneity with respect to  
local tag reads.

while ratio calculation is rather trivial in chip-chip the same is not  
trivial -at least to me- in chipseq. is there a kind of common opinion  
on how to perform these steps without having to manipulate the raw  
data too much? how do you, for example, treat tag-free regions in the  
input material?

i would also like to point out that i would be interested in a  
solution that is not based on any kind of peak detection as -in fact-  
there are many targets that are associated with DNA in non-peaking  
fashion.

any suggestions are very much appreciated
T.


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Tobias Straub   ++4989218075439   Adolf-Butenandt-Institute, München D