Hello Noboru,
Sure, like MACS, USeq uses a window based scan. It doesn't look at peak
shape so it will work equally as well for chIP TFs as histone marks. For
broad peaks just increase the window size to 1-5kb. You might want to try a
range of window sizes. This is internally controlled so any enrichment seen
is likely real regardless of the window size. There's no penalty here.
That said though, it's easy to get any app to return more regions than
another, just drop the thresholds. Remember the FDR estimations are just
that, estimations, not absolutes. So an FDR of 5% in one app might really
be 50% in another. This is why I built in two different FDR estimators in
USeq based on two very different methods (an empirical null created from the
input data and a q-value conversion of the binomial pvalues). Most often
they are in agreement, when they differ significantly I get suspicious of
the results.
Are you generating biological replicas? I'd recommend doing so for your
next set of experiments. 3 chIPs and 3 inputs (or better yet chIPs under
different conditions/ time point) can really help tease out true and false
positives. Dynamic maps also help narrow down the list of marked sites to
those most biologically interesting.
Good luck!
-cheers, D
On 1/5/11 3:43 PM, "Noboru Jo Sakabe" <ns...@uc...> wrote:
> Hi David, to keep the list organized, I'm starting a new thread.
>
> What is your take on using Useq to call peaks on histone data? I've
> been using it and while MACS often does not find peaks in my samples,
> which seem to be poorly enriched, Useq does. But histone modifications
> are different than TF, do you think I can trust Useq for histones?
> Thank you.
>
> noboru
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