This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Cut off for "dist.seqs" and "cluster" step in MOTHUR for "genus" level analysis

Hi community!!! I want to compare the control and test samples at “Genus” level. Can anyone please tell me what cut off should I use at dist.seqs and cluster step? Thanks and Regards, DC7

mothur 16s metagenome
• 1,851 views • link
written by dpc dpc

Usually mothur is used for obtaining an abundance table and the downstream analysis is usually done with other packages like phyloseq

• 0 views • link
written by Asaf Asaf

Sir, I'm confused. Because, in Phyloseq the import_mothur functions import the taxonomy file, shared file and tree file. For generating these three files shouldn't execute these steps?

Thanks, DC7

• 0 views • link
written by dpc dpc

Yes, but it's unrelated to the genus level analysis. Just use the default 0.03 for dist.seqs. Each OTU gets a taxonomic identification (if available), you might get multiple OTUs per genus.

• 0 views • link
written by Asaf Asaf

Sir, can I do phylotype analysis at different taxa levels? Because, if I do OTU analysis at different cutoffs, I am getting a single genus multiple times in the heatmap. Also, after phylotype analysis I am getting 34 classified genus. Do you think 34 is a very low number of genus? May there be any problem with my analysis? Or, 34 is normal for gut microbiome?

Thanks, DC7

• 0 views • link
written by dpc dpc

0 answers

No answers yet.

Log in to answer this question.

More posts like this