Updating previous braker.gtf with addUTR output for non-fungal eukaryotic genome

[sadikmu]

In the first round BRAKER run

braker.pl \
--species=species \
--genome=genome.fna \
--hints=prothint_augustus.gff \
--bam=RNASeq.sorted.bam \
--etpmode \
--softmasking \
--AUGUSTUS_ab_initio \
--cores 8 \
--workingdir $wd_etpmode \
--nocleanup 

Following BRAKER documentation to add UTR

Modify augustus.hints.gtf to point to the AUGUSTUS predictions with hints from previous BRAKER run; modify flaning_DNA value to the flanking region from the log file of your previous BRAKER run; modify some_new_working_directory to the location where BRAKER should store results of the additional BRAKER run; modify somespecies to the species name used in your previous BRAKER run.

BRAKER run for generating UTR parameter in the second round using augustus.hints.gtf and --species name from previous run

braker.pl \
--genome=genome.fna \
--species=species \
--addUTR=on \
--softmasking \
--bam=RNAseq.sorted.bam \
--workingdir=$wd_utr \
--AUGUSTUS_hints_preds=path-to-$wd_etpmode/augustus.hints.gtf \
--cores=8 \
--skipAllTraining

And this generated augustus.hints_utr.gtf as expected. I wanted to add this to braker.gtf generated in the first round run and update the final braker combined prediction as suggested here https://github.com/Gaius-Augustus/BRAKER/issues/331#issuecomment-815275409

Any suggestion, please?

[tomasbruna]

Hello @sadikmu,

there is currently no easy way to do this because the format of braker.gtf is not compatible with UTR procedure.

How many extra genes do you have in braker.gtf compared to augustus.hints.gtf? In case it's not many genes, it should be OK to just use augustus.hints_utr.gtf and add the extra genes from braker.gtf to the result (the extra genes will have GeneMark.hmm in the second column).

Tomas