Extract reference reads

[Nicholas_Bokulich]

@zhang_sonic

The 99_otus was downloaded from the green tree 13_8 version. But the problem here is I is taking few days and the run still has finished yet, I feel like there must be something wrong with it.

See this post. The primer sequences that you are using look like they contain much more than the primers — they also contain linker sequences, perhaps barcode, and other sequences that are non-biological and will not align to your reference. This will cause extraction to fail.

@zhang_sonic

Then I was thinking maybe I will just skip the extract-read part and use the 99_otus_non-aligned.qza to doing the following job. And the second question is how do you think its gonna affect the results?

See here

Good luck!