[Genome] GenScan UCSC track for the ENCODE regions

[Jim Kent]

You also might want to convert the genscan to GFF, and upload as
a custom track to visually compare the sets.  Possibly it's
something in the conversion of the Sn/Sp calculations rather
than the GenScan run itself that is different.


On Oct 5, 2006, at 6:07 PM, 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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