BRAKER with bam files and external proteins

[enriquepola1996]

Hello, I am using BRAKER for the first time to annotate the genome of a plant with an approximate genome of 3Gbp. I have RNA-seq data and a fasta file of proteins from a plant of the same species and it asks me if there are recommendations in my script to obtain good results. I am running the following script on a cluster:

`#!/bin/bash

PBS -N braker_plant

PBS -l nodes=1:ppn=20,vmem=64gb,walltime=700:00:00

PBS -o braker_output.log

PBS -e braker_error.log

module

module load BRAKER/2.1.6

module load augustus/2.5.5

bin and scripts Augustus

export AUGUSTUS_CONFIG_PATH="/clus/usuario/braker/augustus_config"

Directory

cd $PBS_O_WORKDIR

Llama a braker.pl

braker.pl --species=agave --genome=../agusplant.fasta \ --prot_seq=desme.protein.fa --gff3 --cores 20 \ --bam=CP148H_001_sorted.bam --etpmode`

I also wanted to ask if it is advisable to add more than one bam file, in terms of annotation quality.

Could you give me recommendations? I'll be very greatful.

[KatharinaHoff]

It looks like an outdated version of BRAKER. I recommend updating. (--cores was replaced by --threads a while ago, but there were more important changes under the hood)

[enriquepola1996]

Thank you very much.