# KneadData unmatched paired reads

**URL:** <https://forum.biobakery.org/t/kneaddata-unmatched-paired-reads/8758>\
**Category:** KneadData\
**Created:** [February 5, 2026, 2:26pm UTC](https://forum.biobakery.org/t/kneaddata-unmatched-paired-reads/8758 "2026-02-05T14:26:50Z")\
**Posts on this page:** 1\
**Showing post:** 3

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**Author:** ![lfreund](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/lfreund/32/3046_2.png) [@lfreund](https://forum.biobakery.org/u/lfreund)\
**Post date:** [February 20, 2026, 9:34pm UTC](https://forum.biobakery.org/t/kneaddata-unmatched-paired-reads/8758/3 "2026-02-20T21:34:18Z")

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Hi there, I’ve been having this same issue and I think you’re correct, the read headers need to be changed for KneadData to work (i.e., I downloaded these sequence data from SRA and found this to be the case).

There are some solutions here: [All paired-end read unmatched - #21 by jorondo1](https://forum.biobakery.org/t/all-paired-end-read-unmatched/2895/21)

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