Re: [Useq-users] Problem with options for ChipSeq application

[David N. <dav...@gm...>]

Ah, thanks for catching that, I¹ll add this back into the next SourceForge
release, 7.6.3.  I should get that posted later today or tomorrow.

As for your run, 7 reduced regions is rather a low number.  Are you
performing a chIP vs chIP or a chIP vs Input analysis?

You can run the individual applications that the ChIPSeq app wraps, notably
run the EnrichedRegionMaker with the ­n option to output a set number of
peaks.  Check out the tutorial/ user guide for details.

-cheers, D



On 1/24/11 2:07 PM, "Ketaki Bhide" <kb...@il...> wrote:

> Hello,
>             I used ChipSeq application of Useq. I had following
> questions regarding the same:
> 
> Q. I was not able to set up the window size by typing in -w while
> running ChipSeq application.
> It gave me an error of -w is not an option. Please let me know right
> parameter to set the window size
> 
> Q.Eventually I want to compare the USeq ChipSeq's application with
> some other software.
> It becomes really hard to compare peaks for my data since Useq
> application just gave 7 reduced regions with default
> parameters while other sofware gave me several present on different
> chromosomes.
> Could you please let me know which parameters need to be changed to
> get maximum number of peaks from USeq's ChipSeq application.
> 
> 
> Regards
> Ketaki Bhide
> 
> 
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