hi everyone

I am working on transcriptomics analysis in flowering plants. I want to detect alternative splicing in flowering plants, to detect splicing I am using rmats software, here I have settled all dependencies. Now I am facing problem in input file, mainly how to arrange bam file in txt file. I have different species bam and gtf files. There confusion in b1 and b2 during run file if I have 1 species and 1 gtf file then how can add species to during running time. If I am wrong then guide me to make a correct input file.