[maker-devel] understanding maker output

[Marion Dubarry]

Dear Maker,

I have some issue understanding the output of maker. I ran Maker on a 
chromosome where I already know the number of expected genes (1332) .

1) I ran Maker with mrna.gff and prot.gff files and Snap (est2genome=1 
protein2genome=1) and I try also with just Snap, and I obtain the same 
files, why ? I was expected that with just ab initio or experimental 
data, the results would have been different !

In the folder /chr3.maker.output/chr3_datastore/50/43/chr3 I have 
different files :
     chr3.gff
     chr3.maker.non_overlapping_ab_initio.transcripts.fasta
     chr3.maker.snap_masked.transcripts.fasta
     theVoid.chr3/
     chr3.maker.non_overlapping_ab_initio.proteins.fasta
     chr3.maker.snap_masked.proteins.fasta
     run.log

2) All of fasta files contains 1263 sequences, while the gff file 
contains 87178 matches. Why there is a so big differences between my files ?
In my gff file, line with column 2 = "snap_masked" and column 3 = 
"match" correspond to the 1263 models in fasta files. To what correspond 
the  "repeatmasker" and "repeatrunner" matches ?


Thanks in advance,
Marion