Which file should I use as a result?

[jwli-code]

hi， This is my code. I don't know if this is correct, but my target species is Brassica napus.I wonder if this software only scores intron boundaries, and if there is a filtered result for this score. The last files generated in outdir are hc.gff miniprot.gtf miniprothint.gff miniprot_representatives.gff miniprot_representatives.gtf miniprot_trainingGenes.gff miniprot_trainingGenes.gtf .I don't know which one I should use most of the final gff file annotation results I want.

mkdir log
mkdir result
cd result/
#micromamba activate miniprot
#bsub -J index -n 20 -o ../log/index.out -e ../log/index.err -R span[hosts=1] -q normal \
#"
#miniprot -t 20 -d Bna_ZS11_v0.0.mpi Bna_ZS11_v0.0.fasta
#"
cat ../list.txt |while read line;
do
bsub -J ${line} -n 2 -o ../log/${line}_score.out -e ../log/${line}_score.err -R span[hosts=1] -q normal \
"
#miniprot -t 20 -Iu --aln Bna_ZS11_v0.0.mpi ${line}.pep >../result/${line}.aln
module load GCC/4.9.2
#../miniprot-boundary-scorer/miniprot_boundary_scorer -o ../result/${line}miniprot_parsed.gff -s ../miniprot-boundary-scorer/test/test_files/blosum62_1.csv < ../result/${line}.aln
../miniprothint/miniprothint.py ${line}miniprot_parsed.gff --workdir ${line}hint
"
done

[tomasbruna]

Hi @jwli-code,

you can use miniprothint.gff as the "final" result. hc.gff is a subset of miniprothint.gff that passes more stringent thresholds - that would be the "filtered" result you are looking for.

The remaining output files are intended for use by various gene prediction tools such as GALBA.

I wonder if this software only scores intron boundaries

The software predicts all coding exon boundaries, i.e., start and stop codons are also predicted and scored in the output.

I don't know which one I should use most of the final gff file annotation results I want.

Note that miniprothint does not aim to produce a "final genome annotation". Its result, gene prediction hints, serves as an input to other gene predictors that can utilize the hints when predicting full gene structures.

[francicco]

Hi,

Can I use it with BRAKER? In case, which flag should I use? Cheers F

[KatharinaHoff]

miniprothint is integrated in GALBA, not in BRAKER.

Francesco Cicconardi @.***> schrieb am Do. 18. Jan. 2024 um 13:18:

Hi,

Can I use it with BRAKER? In case, which flag should I use? Cheers F

— Reply to this email directly, view it on GitHub https://github.com/tomasbruna/miniprothint/issues/1#issuecomment-1898464615, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJMC6JBK5TSRVO735ZKS3STYPEOJFAVCNFSM6AAAAABBWBJH7KVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOJYGQ3DINRRGU . You are receiving this because you are subscribed to this thread.Message ID: @.***>