[maker-devel] understanding maker output

[Carson Holt]

Hi Marion,

None of your evidence supported any of the SNAP models, so you got no results. You did have reference SNAP models in both fasta and GFF3 format (matych/match_part features), but those are just for reference.

You probably have issues with either your mrna.gff or prot.gff files.

You may want to familiarize yourself with how MAKER works and expected output using an online tutorial like the following —> http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014 <http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014>

—Carson



> On Mar 16, 2016, at 9:09 AM, Marion Dubarry <mdubarry at genoscope.cns.fr> wrote:
> 
> 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
> 
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