Hmm, that's a bit worrying. There's no need to balance reads with USeq.
This is internally controlled. More data should increase the number of
regions returned at a given FDR, not decrease it. Your result is rather odd?
Would you mind posting the data to a web accessible directory somewhere.
Label it chIP and Input and let me know what genome build it is, I'd like to
run some tests.
-cheers, D
On 1/5/11 3:41 PM, "Noboru Jo Sakabe" <ns...@uc...> wrote:
> Hi David, I ran Useq on a sample that has a lot fewer reads than input.
> I got very few peaks.
> Then I balanced treatment and input, randomly selecting reads from
> input.
> Then I got ~14k peaks at FDR 4%. QuEST had also found a similar
> number of peaks.
> I know that balancing reads is an issue in MACS, I would like to
> know if this is also true for Useq. I believe it is, given my results,
> but could you comment on this?
> Thank you!
>
> noboru
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