can forward and reverse reads be truncated to different lengths?

Hi yipinto,

I got low quality reverse reads as well and was considering joining reads with different trimming length for forward and reverse reads. Not sure whether i can do it with QIIME2. Just wondering whether you solved your problem. Would you mind letting me know the strategy you used?

Thanks,

jia

Sure, the forward and reverse reads definitely do not need to be trimmed/truncated at the same sites. That is why dada2 denoise-paired has separate trim and truncate parameters for the forward and reverse reads.

You do not need to truncate and a uniform position either; you can use the --p-trunc-q parameter to truncate based on a Q-score threshold.

In either case, dada2 will join these reads if there is still sufficient overlap (min 12 nt).

If the reverse reads are that bad you may just want to scrap the reverse reads and focus on the better-quality forward reads…

Hi Nicholas,

Thanks for the quick response. That’s really helpful!

Thanks,

Jia

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