useq-users

[Useq-users] Problem with options for ChipSeq application

[Ketaki B. <kb...@il...>]

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

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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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
> 
> 
> ------------------------------------------------------------------------------
> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
> Finally, a world-class log management solution at an even better price-free!
> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> February 28th, so secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsight-sfd2d
> _______________________________________________
> Useq-users mailing list
> Use...@li...
> https://lists.sourceforge.net/lists/listinfo/useq-users