I am currently starting to use the BRAKER2 pipeline for gene prediction in the genomes of two Phytophthora species. For those who don't know about the pipeline, BRAKER2 uses RNA-seq alignments as input to train GeneMark and AUGUSTUS ab initio gene predictors.
Since I only have RNA-seq data for one of the genomes, I was wondering if it would be a good idea to use RNA-seq reads from a closely related species for my case. Also, do you have any suggestions I could use when running this pipeline? I don't have much experience in annotation, so any idea would be appreciated.
Thank you very much in advance!