I am interested in getting the number of reads unaligned after nucleotide alignment (relative to my input reads) and the number of reads unaligned after translated alignment, from the humann3 log file. However, I am not sure if what I think is correct.
For example, if I get 75% of unaligned reads after nucleotide alignment, does that mean that 75% of my input reads do not align ?
And if after that I get 60% of unaligned reads after translated alignment, does that mean 60% of my previous 75% do not align or does it mean that for the entire process 60% of my input reads do not align ?
Sorry for my naïve and confused question and thanks for your help