Tutorial:Training GeneMark-EP+ ab-initio tool
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19 months ago
Juke34 ★ 6.3k

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 sucessfully :

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

annotation genemark training abinitio Tutorial • 543 views
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