Entering edit mode
4.5 years ago
dpc
▴
250
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
Usually mothur is used for obtaining an abundance table and the downstream analysis is usually done with other packages like phyloseq
Sir, I'm confused. Because, in
Phyloseq
theimport_mothur
functions import thetaxonomy
file,shared
file andtree file
. For generating these three files shouldn't execute these steps?Thanks, DC7
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.
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