otu.hierarchy
The otu.hierarchy command relates OTUs at different distances
Default settings
There are two ways to use the otu.hierarchy command. You can compare clusters from 2 different distances, or create a cons.taxonomy file relating ASVs to OTUs.
To relate OTUs from 2 different distances, run the following:
A list file and two labels must be inputted for this method
mothur > otu.hierarchy(list=final.opti_mcc.list, label=0.03-0.05)
In the final.opti_mcc.0.03-0.05.otu.hierarchy output file, the first column is what the OTU looked like at distance 0.05 followed by the list of sequences in the OTUs at distance 0.03 that merged together.
To find the classifications and OTUs your ASVs belong to, run the following:
mothur > make.shared(count=count=final.count_table) - create an ASV list and shared file
mothur > cluster.split(fasta=final.fasta, taxonomy=final.taxonomy, count=final.count_table) - create distance based OTU list file
mothur > otu.hierarchy(list=final.opti_mcc.list, asvlist=final.asv.list, taxonomy=final.taxonomy, count=final.count_table)
The output file, final.opti_mcc.ASV_0.03.asv.cons.taxonomy, will look like:
ASVLabel ASV_Abundance Taxonomy_OTULabel
ASV0001 12196 Bacteria;"Bacteroidetes";"Bacteroidia";"Bacteroidales";"Porphyromonadaceae";"Porphyromonadaceae"_unclassified;Otu001;
ASV0002 8829 Bacteria;"Bacteroidetes";"Bacteroidia";"Bacteroidales";"Porphyromonadaceae";"Porphyromonadaceae"_unclassified;Otu002;
ASV0003 7698 Bacteria;"Bacteroidetes";"Bacteroidia";"Bacteroidales";"Porphyromonadaceae";"Porphyromonadaceae"_unclassified;Otu003;
ASV0004 7436 Bacteria;"Bacteroidetes";"Bacteroidia";"Bacteroidales";"Porphyromonadaceae";Barnesiella;Otu004;
...
Options
The output parameter allows you to either specify the output to display the names of the sequences in the otus or the otu numbers, the default is name.
mothur > otu.hierarchy(list=final.opti_mcc.list, label=0.03-0.05, output=otulabel)
Otu001 Otu001 Otu219 Otu226 Otu266 Otu271 Otu297 Otu336 Otu377 Otu409
Otu002 Otu006 Otu009 Otu237 Otu252 Otu270 Otu277 Otu341 Otu385
Otu003 Otu002 Otu213 Otu241 Otu279 Otu302 Otu334 Otu417
...
So Otu003 at distance 0.05 is made up of OTUs Otu002, Otu213, Otu241, Otu279, Otu302, Otu334 and Otu417 at distance 0.03.
Revisions
1.46.0 - Adds ASV to OTU mapping for otu.hierarchy command. #777