Rarefaction curves

Commands in mothur
1

Hey,

I’m new to Mothur and was looking to use rarefaction curves to reduce the number of OTUs to focus on. I am less concerned about the richness across samples (because OTUs that are only found in a single sample, but at high relative abundance are actually important) and more concerned with straight relative abundance and was looking for any advice on how to go about this?

Thanks so much!

Gemma

2

Hi Gemma,

You can run rarefaction.single to generate the files you need. If you look at the MiSeq SOP page, you’ll see where this command fits in with everything else.

Pat