# Paired end files processing

**URL:** https://forum.biobakery.org/t/paired-end-files-processing/2809
**Category:** MetaPhlAn
**Created:** [November 18, 2021, 7:36am UTC](https://forum.biobakery.org/t/paired-end-files-processing/2809 "2021-11-18T07:36:05Z")
**Posts on this page:** 2
**Page:** 1

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### Author: ![saras22](https://avatars.discourse-cdn.com/v4/letter/s/59ef9b/32.png) [@saras22](https://forum.biobakery.org/u/saras22)
#### Post date: [November 18, 2021, 7:36am UTC](https://forum.biobakery.org/t/paired-end-files-processing/2809/1 "2021-11-18T07:36:06Z")

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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](https://forum.biobakery.org/t/paired-end-reads-in-metaphlan3/676)) 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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### Author: ![fbeghini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fbeghini/32/81_2.png) [@fbeghini](https://forum.biobakery.org/u/fbeghini)
#### Post date: [December 3, 2021, 1:25pm UTC](https://forum.biobakery.org/t/paired-end-files-processing/2809/2 "2021-12-03T13:25:39Z")

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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.