I have classified OTUs using this command
mothur > classify.otu(list=final.agc.list, count=final.count_table, taxonomy=final.taxonomy, label=0.03)
I got two output files: a taxonomy file and a tax.summary file.
In the cluster.split command i has used tax level 4 as follows
cluster.split(fasta=final.fasta, count=final.count_table, taxonomy=final.taxonomy, taxlevel=4, cluster=f
After this i clustered the sequences into OTUs using Vsearch.
My first question is about tax level. Using tax level=4 i got the following tax.summary table
In the tax level column its going up to 6 but i had set tax level=4. Can someone please explain how to interpret the information in this table and what it means? This table is in detailed format.
I have also generated the same table with simple format as follows
The above picture shows simple format. Moving along the table horizontally there were more columns in this simple format. water neg shows the last sample. What are these columns generated next to it?
How to interpret the information in this simple format table?
My second question is
I want to generate two tables, one with taxonomic classification upto genus level and another table with taxonomic classification upto Phylum level. How can i do that?
I hope i was able to explain my questions clearly.