Open YanisChrys opened 5 months ago
Hello,
In order to better annotate my reptile genome I have used BRAKER3-ETP and Galba (with ~6 of the closest relative proteomes) and now I am trying to combine them using TSEBRA. The inputs look like this:
BRAKER3 | C:67.6%[S:56.0%,D:11.6%],F:3.6%,M:28.8%,n:7480
GALBA | C:93.3%[S:75.1%,D:18.2%],F:1.6%,M:5.1%,n:7480
This is the command I am using:
singularity exec --bind $WORKDIR /path/to/containers/braker3.sif /opt/TSEBRA/bin/tsebra.py \ --gtf ${galba_gtf},${braker_gtf} \ --hintfiles ${hints_gff2},${hints_gff1} \ --filter_single_exon_genes \ --ignore_tx_phase \ --cfg ${braker_cfg} \ --out ${out_gtf} \ --verbose 1 2> ${log}
I have experimented a lot but I can't find a way to run it that maximises busco and keeps mostly single genes. I have tried the following:
Using different config files and thresolds:
However these all result in a lot of duplicates (65-87%) and only slightly better busco than galba (92-94%).
Decreasing the e_n values, reduces duplicates but also the busco score.
Perhaps the issue is with transcripts having equally low support so more than 1 overlapping transcripts are kept?
Any advice is welcome. Please feel free to ask for any extra information or log files.
Hello,
In order to better annotate my reptile genome I have used BRAKER3-ETP and Galba (with ~6 of the closest relative proteomes) and now I am trying to combine them using TSEBRA. The inputs look like this:
BRAKER3 | C:67.6%[S:56.0%,D:11.6%],F:3.6%,M:28.8%,n:7480
GALBA | C:93.3%[S:75.1%,D:18.2%],F:1.6%,M:5.1%,n:7480
This is the command I am using:
I have experimented a lot but I can't find a way to run it that maximises busco and keeps mostly single genes. I have tried the following:
Using different config files and thresolds:
However these all result in a lot of duplicates (65-87%) and only slightly better busco than galba (92-94%).
Decreasing the e_n values, reduces duplicates but also the busco score.
Perhaps the issue is with transcripts having equally low support so more than 1 overlapping transcripts are kept?
Any advice is welcome. Please feel free to ask for any extra information or log files.