# All paired-end read unmatched

**URL:** <https://forum.biobakery.org/t/all-paired-end-read-unmatched/2895>\
**Category:** KneadData\
**Created:** [December 13, 2021, 1:29am UTC](https://forum.biobakery.org/t/all-paired-end-read-unmatched/2895 "2021-12-13T01:29:42Z")\
**Posts on this page:** 1\
**Showing post:** 32

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**Author:** ![Zoexfq](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/zoexfq/32/2941_2.png) [@Zoexfq](https://forum.biobakery.org/u/Zoexfq)\
**Post date:** [July 15, 2024, 5:29am UTC](https://forum.biobakery.org/t/all-paired-end-read-unmatched/2895/32 "2024-07-15T05:29:51Z")

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Hi, I just came across the same issue.

When using KneadData, it appears that the software first outputs a SAM file and then processes this file to determine the mapping results. My understanding is that during this post-processing step, the software identifies paired reads by examining the suffix of each read’s name, looking for either ‘/1’ or ‘/2’ to differentiate between the two ends of a pair.

While this approach works seamlessly with raw sequencing data, I have found that when working with data obtained from public databases, the read names are often sanitized, and the distinguishing ‘/1’ or ‘/2’ suffixes are removed. This could potentially lead to misidentification of paired reads during the post-processing phase.

Bowtie2 actually offers built-in options to handle such cases elegantly. The `--un-conc` and `--un` parameters in bowtie2 are specifically designed to output unmapped reads in a way that retains the paired-end information, even when the read names have been altered or are absent of these suffixes.

Could you maybe include an option for users to enable bowtie2’s `--un-conc` and `--un` parameters during the mapping process? This would allow for better handling of paired-end reads with modified names.

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