Paired end files processing

Microbial community profiling MetaPhlAn
1

Hi @fbeghini

  1. 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?

  1. 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
Saraswati Awasthi

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MetaPhlAn does not use paired reads, paired datasets are treated as independent when mapping. You don’t need to concatenate the two files into a new one, you can provide both of them as a comma separated list.

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