Would there be a reason to truncate the forward and reverse reads at different points?

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Hi @msport469,

You can absolutely truncate the forward and reverse in different places if there's a different drop off in quality. I do it often when my forward reads are high quality and the reverse reads have a lower drop in quality. In fact, this is a common behavior in Illumina data.

There is one caveat: If you trim your reverse data too much, you may no longer be able to overlap enough to join the ends. So, just watch your trim length if you want to join reads.

Best,
Justine

P.S. I moved this to user support, since it seems like a more general question. (Community plugin support is where you can go ask about non-core QIIME plugins like q2-PICRUSt).

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