# MetaPhlAn Input for paired end sequences previously filtered?
**URL:** https://forum.biobakery.org/t/metaphlan-input-for-paired-end-sequences-previously-filtered/8557
**Category:** MetaPhlAn
**Created:** [October 17, 2025, 11:12am UTC](https://forum.biobakery.org/t/metaphlan-input-for-paired-end-sequences-previously-filtered/8557 "2025-10-17T11:12:34Z")
**Posts on this page:** 3
**Page:** 1
### Author:  [@Leticia\_gomez](https://forum.biobakery.org/u/Leticia_gomez)
#### Post date: [October 17, 2025, 11:12am UTC](https://forum.biobakery.org/t/metaphlan-input-for-paired-end-sequences-previously-filtered/8557/1 "2025-10-17T11:12:34Z")
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?
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### Author:  [@Claudia\_Mengoni](https://forum.biobakery.org/u/Claudia_Mengoni)
#### Post date: [October 20, 2025, 12:28pm UTC](https://forum.biobakery.org/t/metaphlan-input-for-paired-end-sequences-previously-filtered/8557/2 "2025-10-20T12:28:05Z")
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`).
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### Author:  [@Leticia\_gomez](https://forum.biobakery.org/u/Leticia_gomez)
#### Post date: [October 20, 2025, 4:10pm UTC](https://forum.biobakery.org/t/metaphlan-input-for-paired-end-sequences-previously-filtered/8557/3 "2025-10-20T16:10:55Z")
Thank you for the info!!