Hello community, Pat
I have a question regarding the clustering steps to generate OTUs. I am analyzing a 18S-V4, MiSeq data set.

I used cluster.split as recommended by the MiSeq SOP, but then wanted to use get.oturep, command that requires a .dist file.

Should I just run dist.seqs()? If so, any caveats about the file inputs I should be aware of?

Thanks for the help, I am new and get easily confused when making decisions on what is accurate.


I would probably encourage you to use method=abundance in get.oturep instead of a distance matrix. The distance approach tends to suck up large amounts of RAM and give essentially the same values as the abundance approach.


Thanks Pat, will try that.