I have RNA seq data of 12 samples (paired end, so 24 files) and I ran tophat2 for alignment on all of them which gave me one bam file for all the samples. Now I need separate bam files for all the samples. Can I spilt them from the one I have or I have to do tophat2 for all the samples separately? If yes, how to do it.
I need them for FRASER (spilicing detction) I would also appreciate if anyone used FRASER before could help me a bit to get started. I am working with plant data for the first time.