[Genome] GenScan UCSC track for the ENCODE regions

[Paul Flicek]

Hi Axel,

I did all of the evaluations for the EGASP paper (they were also done  
by JF Abril to ensure that the results were correct).  I just double  
checked the Genscan predictions we used for the paper and they are  
exactly the standard ones that are available for download at UCSC.

I'm not sure if the gsBig front end results in the effects you are  
seeing comparing your results to a local genscan copy, but Genscan's  
results can be sensitive to the masked sequence used.  I would  
recommend using the same masked sequence that UCSC uses if you are  
not doing that already.

Please feel free to contact me off the list if you want more  
information about what we did for the EGASP paper evaluations.

Thanks,
Paul


/************************************/
Paul Flicek
European Bioinformatics Institute
Hinxton, Cambridge, UK
http://www.ensembl.org


On 6 Oct 2006, at 02:07, Axel E. Bernal wrote:

>
> Hi,
>
> I am trying to reproduce the predictions of the GenScan track for the
> ENCODE region.
> The numbers for the nucleotide level, as they appeared in the last  
> EGASP
> '05 ENCODE publication: Genome Biology, Volumen 7, Supplement 1,  
> are as
> follows (they appear in page S2.10 under "USCS genscan track"):
> Sn:84.17%
> Sp:60.60%
>
> Whereas the ones that I obtained with a local copy of GenScan are  
> around:
> Sn:48.92%
> Sp:59.40%
>
> I made sure no errors were made while reading the output of the  
> program,
> also I am using masked sequences - I used RepeatMasker - (the  
> results with
> unmasked sequences are even worse).
>
> I'd appreciate if you could help me out as to what could be the  
> reason I
> am obtaining these bad results on ENCODE; in all other test sets I  
> don't
> have this problem. Did you use any especial parameters for running the
> program? or any pre/post-processing in the sequences?
>
> Thanks a lot in advance,
>
> Sincerely,
>
> Axel E Bernal
> University of Pennsylvania
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