Why do I loose 36.8% of reads while using PEAR for merging?

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Let's take a look at this step:

qiime vsearch join-pairs
--i-demultiplexed-seqs 02_analyses/seqs/paired.qza
--o-joined-sequences 02_analyses/demux/demux-joined.qza.

Add the --verbose setting, and rerun that step, and post the new data --verbose provides. That will give us more diagnostic data about how well joining worked, as shown in the example data I posted.

We can also look at the quality of the joinined reads using FastQC or qiime demux summarize, but that vsearch log will give us the best clues!

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