Hi, I am looking into Dual RNA-SEQ. As far as I understand so far, I am gonna end up with FASTQ file(s) that contain(s) reads from both organisms.
It is plausible to think that I can separate the two by using some specific settings in HISAT2? Or other aligners? Or are there better tools for this job? I know is a complicated subject and there are many ways of approaching the situation. I can tell that there are not clear lines when it comes to Dual RNA-SEQ. However, I just want to know if I am going in the right direction.