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
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