# Single-end or Paired-end?

**URL:** https://forum.biobakery.org/t/single-end-or-paired-end/6097
**Category:** KneadData
**Created:** [October 20, 2023, 2:22pm UTC](https://forum.biobakery.org/t/single-end-or-paired-end/6097 "2023-10-20T14:22:10Z")
**Posts on this page:** 1
**Page:** 1

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### Author: ![gsidhu](https://avatars.discourse-cdn.com/v4/letter/g/97f17d/32.png) [@gsidhu](https://forum.biobakery.org/u/gsidhu)
#### Post date: [October 20, 2023, 2:22pm UTC](https://forum.biobakery.org/t/single-end-or-paired-end/6097/1 "2023-10-20T14:22:10Z")

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I want to run Kneaddata on bacterial shotgun sequences and then Humann 3 on filtered sequences. I have paired-end FASTQ files.

I understand that Humann will not pair the reads and analyze paired-end reads as single-end reads (I plan to concatenate two files before running Humann).

My question is, should I run Kneaddata in single-end or paired-end mode? Since, Humann will consider only one read at a time, it does not matter if paired mate is present or not. Correct?