[Genome] GenScan UCSC track for the ENCODE regions

[Axel E. Bernal]

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