I'm interested in conducting gene prediction for a plant genome using RNA sequencing data. To achieve this, I intend to perform RNA sequencing alignment and employ BRAKER2 for gene prediction. Before running BRAKER2, I'm considering applying soft-masking to the genome. I would like to clarify whether I should perform masking before creating the BAM alignment file or if it's possible to align the RNA sequencing reads with the genome without masking. I thought it should not matter for RNA-seq data because they are coming from exons which I assume contains no long-range repeats.
Request your suggestion/guidance.
Thank you in advance.