I have total 300 fastq.gz files from 150 samples (one forward-end and one reverse-end read each sample). I want to profile them samplwise with MetaphlAn3. I will run them using
for loop. Is there any problem if I first, concatenate the forward and the reverse files of each of the sample and get 150 fastq.gz files. And, then run these 150 fastq.gz files with MetaPhlAn3?
Thanks and regards,