Cut off for "dist.seqs" and "cluster" step in MOTHUR for "genus" level analysis

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3.8 years ago

dpc ▴ 240

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 • 1.1k views

ADD COMMENT • link 3.8 years ago by dpc ▴ 240

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

ADD REPLY • link 3.8 years ago by Asaf 10k

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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

ADD REPLY • link 3.8 years ago by dpc ▴ 240

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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.

ADD REPLY • link 3.8 years ago by Asaf 10k

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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

ADD REPLY • link 3.8 years ago by dpc ▴ 240

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