Lose many reads after running cut-adapt and join-pairs

[SoilRotifer (Mike Robeson)]

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

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: https://forum.qiime2.org/t/the-results-of-dada2-after-cutadapt-showed-that-there-were-still-primers/19194/4 https://forum.qiime2.org/t/remove-primer-in-paired-end-demultiplexed-file/17376/12 -Mike

Finally, if these do not help, you may want to consider using only the forward read as outline in Hguyen et al. 2015.

-Mike