I’ve noticed that diamond step takes quite long time, and so I ran my samples with -bypass translated search. Unfortunately, the mapping rate is not so great. Therefore, I would like to try again with translated search at this time. My questions is, can I do this with current intermediate and output files?
I thought the manual 2.6 (humann3 · biobakery/biobakery Wiki · GitHub) could be relevant, and I tried it using my bowtie intermediate file (bowtie2_aligned.sam) as an input. However, the outputs are anyway same as the one I had before with bypass flag. Perhaps, I was trying something irrelevant. I would very appreciate if you could help me get through it.