Using DADA2, losing 50% of reads after filtering and 80% of reads by the end

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Hi Andrew,
I would love to know the answer for that too - we are having similar issues with faecal/caecal samples using the EMP protocol to the detail with V4-V5 primers (example below). Which protocol are you using for your library prep?

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Sorry I don't have an answer (yet), we are currently running some tests.

Best wishes,

Francine