[maker-devel] Annotation quality and converting gff3 to gtf

[James Eckert]

Hello,

I'm currently trying to figure out ways to evaluate the quality of
annotations that MAKER produces. I'm working on a novel species, so there
isn't a reference genome to compare the annotation quality to.

After doing a bit of searching on the web, I came across the EVAL tool,
which I thought may be useful for checking the output quality. EVAL takes
in gtf files, not gff3, however MAKER seems to have addressed this problem
through its accessory scripts.

I first used the script "gff3_merge" to have my whole annotation under one
gff3 file. Next I used "add_utr_start_stop_gff". This would explicitly add
the UTRs, which would be needed for converting the gff3 file to gtf. The
problem arose when trying to run "gff3_to_eval_gtf". I was expecting MAKER
to process the whole gff3 file, but it seems to have only processed 2
nodes. The same thing happens when running the "gff3_2_gtf" script.

Here is the command I'm running, along with the output:
gff3_to_eval_gtf assem_kmer_57_utr.gff3
NODE_20666_length_66353_cov_18.405483    maker    CDS    8801    8984
.    -    0    gene_id "1"; transcript_id "2";
NODE_20666_length_66353_cov_18.405483    maker    CDS    8113    8717
.    -    2    gene_id "1"; transcript_id "2";

My question is whether the "gff3_to_eval_gtf" and "gff3_2_gtf" scripts have
a bug in them, or whether I'm just doing the process wrong? Perhaps if the
conversion doesn't work, there exists an alternative to EVAL that works
with native MAKER annotations?

Attached is my whole genome gff3 file, along with the file I ran
"gff3_to_eval_gtf" on.
 assem_kmer-57_exp-44_covcutoff-auto_contigs.all.gff3<https://docs.google.com/file/d/0Byl5QhezwxYOUFFBMVpldFJOb28/edit?usp=drive_web>

 assem_kmer_57_utr.gff3<https://docs.google.com/file/d/0Byl5QhezwxYOYjBOWlVWMEJpTjQ/edit?usp=drive_web>

Thank you in advance for your help,

James
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