Hi,
I always think I should use IDR from ENCODE to get some <conservative>
peaks from replicates, then move to Diffbind/DESeq.

How do you think?

PS: IDR: https://sites.google.com/site/anshulkundaje/projects/idr

Regards,
Sheng



On Wed, Nov 6, 2013 at 10:18 AM, Davide Cittaro <cittaro.davide@hsr.it>wrote:

> Dear Lucia,
>
> On 05/nov/2013, at 13:57, Giuseppe Gallone <giuseppe.gallone@dpag.ox.ac.uk>
> wrote:
>
> >> I do not recommend doing the peak calling with the pooled data.After
> >> doing several ChIP-seq experiments with replicates I have observed that
> >> a lot of peaks, even ones with high z-scores/low p-values, do not show
> >> up in more than one replicate (but maybe this is particular to my type
> >> of experiments).  Merging all the peaks leads to a high number of false
> >> positives. So you need to integrate the peak locations into a single
> >> file but make sure you have a minimum number of carriers for each peak,
> >> I usually do presence in at least 2 of the replicates.
>
> This sounds reasonable and, indeed, I have a similar anedoctical
> experience. Do you have some data/benchmarks supporting this claim?
> Thanks,
>
> d
>
>
> /*
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