Tutorial:Training GeneMark-EP+ ab-initio tool

Question

[Juke34]

You could decide to use the evidence.gff and prothint.gff files from ProtHint.

In my case I already have an annotation (MAKER evidence-based). So I decided to use the annotation I had.

But it cannot used like that because Genemark uses Intron, start_codon, stop_codon features, which are absent from the MAKER annotation gff file.

So here are the steps to cheat successfully:

Prerequisite: AGAT

# add start and stop codons
agat_sp_add_start_and_stop.pl --gff maker_annotation.gff --fasta genome_sm.fa -o maker_annotation_startstop.gff
# add introns
agat_sp_add_introns.pl --gff maker_annotation_startstop.gff  -o maker_annotation_startstop_introns.gff 
# remove useless features
awk '{if($3=="intron" || $3=="start_codon" || $3=="stop_codon") print $0}' maker_annotation_startstop_introns.gff > maker_annotation_startstop_introns_only.gff
# replace intron by Intron (Otherwise Genemark fails)
sed -i 's/       intron  /       Intron  /' maker_annotation_startstop_introns_only.gff
# add al_score attribute with value over 0.3 otherwise intron features are thrown away
awk '{print $0";al_score=1"}' maker_annotation_startstop_introns_only.gff > maker_annotation_startstop_introns_only_al_score_tag.gff

Now you can run GeneMark:

/path/to/genemark/gmes_petap.pl \
  --evidence maker_annotation_startstop_introns_only_al_score_tag.gff \
  --training -v \
  --sequence genome_sm.fa \
  -cores 16 \
  --EP maker_annotation_startstop_introns_only_al_score_tag.gff