Hi Tobias,
On Jan 15, 2009, at 7:36 AM, Tobias Straub wrote:
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.
I thought it would be relevant to put this paper on your radar, since
it's quite recent and discusses aspects you mention (ratio calculation
in chip-seq as well as copy-dependent heterogeneity w.r.t reads):
PeakSeq enables systematic scoring of ChIP-seq experiments relative to
controls
http://www.nature.com/nbt/journal/v27/n1/full/nbt.1518.html
Unfortunately it still is concerned with peak calling, so I guess its
most appropriate for ChIP for TF binding as opposed to things like
histone modifications. Perhaps it might give you some ideas of how one
might approach ip:input ratios and such, so you might still find it
useful.
HTH,
-steve
--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University
http://cbio.mskcc.org/~lianos
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