- Question 1:
I had asked this question earlier that if metaphlan3 does not use the paired-end information then how does it handle the paired-end files?
- Question 2:
I wanted to do metaphlan3 for multiple paired end files so I concatenated the paired-end files to a single file and did the analysis but I find now that when I am doing it separately, the way it is mentioned the wiki of metaphlan3 to give input of paired-end files separated by a comma the results are coming different. But in an issue raised by @DEEPCHANDA7 (Paired-end reads in MetaPhlAn3) you told that both ways the results would be same. Why is that happening can you explain?
Thanks in Advance