MetaPhlAn Input for paired end sequences previously filtered?

Microbial community profiling MetaPhlAn
1

After filtering my sequences with KneadData, I was wondering which files to use as MetaPhlAn input. I know that I have to put paired_1 and paired_2 separated by comma, but Should I also include the unmatched sequences?

2

Hi @Leticia_gomez,

You can also include the unmatched sequences (e.g. metaphlan file_R1,file_R2,file_unmatched) since MetaPhlAn does not use the paired information (the only exception being if you want to perform paired subsampling with –subsampling_paired).

3

Thank you for the info!!