[maker-devel] Interpreting Maker Results

[Kipp Johnson]

Hi Carson,

      I'm trying to get my genetic annotation out of maker. My maker run on
a non-model eukaryote finished, and I used your gff3_merge script to merge
the resulting files. This file is enormous, because I used snap, augustus,
genemark, repeatmasker, exonerate, and blast, and has a lot of entries from
all of these different programs.

      I want to extract only the genetic regions predicted by maker, so I
used the gff3_merge script with the "-g" option. However, when I do this, I
get a maker file that only has about 12,000 genes, while I was expecting
around 20,000 genes for our genome. However, when I use the fasta merge
tool, however, I get output files (for example,
"merged.fasta.all.maker.non_overlapping_ab_initio.proteins.fasta") with
about 21,000 proteins, which is closer to the gene number that I was
expecting. Does the "-g" option ignore evidence from blast/exonerate or
similar? How should I extract the complete set of genetic regions to blast
against, so that I can go about further working on the annotation?

Also, what is maker using to find these 9,000 extra proteins? Are these
these all alternately sliced or something along those lines? I can't find
any documentation online for how to actually get the final annotations out
of maker correctly.

Thanks for your time!

Best,

     Kipp Johnson
     kippjohnson at uchicago.edu
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