# Lose many reads after running cut-adapt and join-pairs **URL:** \ **Category:** User Support\ **Tags:** vsearch, paired-end, cutadapt\ **Created:** [April 19, 2021, 4:44am UTC](https://forum.qiime2.org/t/lose-many-reads-after-running-cut-adapt-and-join-pairs/19276 "2021-04-19T04:44:34Z")\ **Posts on this page:** 1\ **Showing post:** 3
**Author:** ![SoilRotifer](https://forum.qiime2.org/user_avatar/forum.qiime2.org/soilrotifer/32/21071_2.png) [@SoilRotifer](https://forum.qiime2.org/u/SoilRotifer)\ **Post date:** [April 19, 2021, 2:14pm UTC](https://forum.qiime2.org/t/lose-many-reads-after-running-cut-adapt-and-join-pairs/19276/3 "2021-04-19T14:14:25Z")
Hi @sjcochran, to add to @timanix's excellent advice, I often recommend adding the following flags when running cutadapt: > [@some questions about cutadapt demux-paired](https://forum.qiime2.org/t/some-questions-about-cutadapt-demux-paired/19223/4): > > What primer set and amplicon region are you using? Also, I often recommend that users apply the following flags when using cutadapt: --p-match-read-wildcards \ --p-match-adapter-wildcards \ --p-discard-untrimmed \ For more detail see: -Mike Finally, if these do not help, you may want to consider using only the forward read as outline in [Hguyen _et al_. 2015](http://dx.doi.org/10.1111/nph.12923). -Mike --- _[View the full topic](https://forum.qiime2.org/t/lose-many-reads-after-running-cut-adapt-and-join-pairs/19276)._