[maker-devel] SNAP scores and AED scores

[Masa Roller]

Dear all,

I ran snap2 based gene prediction through maker.

In the resulting gff file, in the source "snap_masked" I can find the 
score in the score column of every snap prediction that did not get 
promoted to a maker gene. This would be the score of how well the 
prediction matches the HMM?

It seems to me that those snap models that are given gene status no 
longer appear as snap_masked source but only as source "maker". Maker 
then removes the score column, instead giving AED and eAED scores (which 
are more about how the model corresponds to the evidence). When viewing 
the maker transcripts and SNAP predictions in a browser, they do not 
match (mostly, maker predictions are longer).

I am interested in the score of individual gene predictions that 
underlined maker gene models. Where could I find that information?

Many thanks!