Hello,
I’m a newbie to Metaphlan. I have a directory of fastq files that I would like Metaphlan to classify. I ran the following code:
for i in *.fastq.gz; do metaphlan $i --input_type fastq --nproc 40 > ${i%.fastq.gz}_profile.txt; done
However, my input fastq files are split into Read1 and Read2 files and the resulting profile.txt files are also split in to Read1 and Read2. I would like the resulting profile.txt files to contain data for the paired reads. Is this possible? Or do I need to somehow interleave the R1 and R1 fastq files before I run them through Metaphlan?
Thank you for your help!