Frequently Asked Questions
If you would like to run this analysis on your own data, make sure to check which V-region was sequenced. In this tutorial, we sequenced the V4 region, and used a corresponding reference for just this region. If you sequenced another V-region, please use an appropriate reference (either the full SILVA reference, or the SILVA reference specific for your region). Similarly, the
Screen.seqs step after the alignment filtered on start and end coordinates of the alignments. These will have to be adjusted to your V-region.
This tutorial was adapted from the mothur MiSeq SOP created by the Schloss lab. Here you can find more information about the mothur tools and file formats. Their FAQ page and Help Forum are also quite useful!