Rarefaction Curves

Commands in mothur
1

I am new to mothur and to these types of analyses. I am trying to produce a rarefaction curve and am uncertain if I should use dereplicated data.

My dereplicated data was produced using the unique.seqs() command. Should I use this file or the full data set including duplicate sequences?

This is part of a pipeline I am building that will culminate in determining richness with the Chao1 estimator.

Thank you

2

When you run the cluster command you will include a name file that will contain the names of all of the redundant sequences. This will then generate the list file that you can use to run your rarefaction and estimation analyses.