Paired-end reads in MetaPhlAn3

Microbial community profiling MetaPhlAn
1

HI @fbeghini
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,
DC7

2

It would be the same as running MetaPhlAn by feeding it with a comma-separated list of file names, eventually they are sequentially piped to bowtie2