We may have just answered our question about closed reference OTU clustering - in the QIIME2 documents for closed reference clustering of features, the parameters section has the following option:
--p-strand TEXT Choices('plus', 'both')
Search plus (i.e., forward) or both (i.e., forward
and reverse complement) strands. [default: 'plus']
We assume if we choose 'both' that would allow for mixed orientation reads?
Next, we were looking for the greengenes reference database for the OTU clustering step. We could not find the 13_8 release on the gg website. We found this post and downloaded the file. Is this is the correct file to use?
The file contains the following folders:
For our closed reference OTU clustering, we need to use one of the xx_otus.fasta files as our reference sequences. Which version should we use - the rep_set or the rep_set_aligned?
Thanks so much!
Lauren :qiime2:
Based on your recommendations above, we would want to use a rooted tree. Which version should we use: XX_otus.tree or xx_otus_unannotated.tree ?