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

[Noboru Jo S. <ns...@uc...>]

    What app are you using? -w works fine for me when using ScanSeqs and 
MultipleReplicaScanSeqs.

    How did you select your peaks (q-value, etc)?
    In my experience, generally Useq finds more peaks than MACS and 
QuEST. I filter by empFDR (and now also by q-value, simultaneously).
    You will have to play with peak width and q-value/empFDR.
    What was the FDR for the other peak callers? Maybe your IP failed?
    How many reads you have? If it was < 10M, read the posts that David 
and I exchanged about balancing reads.


Ketaki Bhide 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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