mothur

ITS data using mothur

I have used mothur for 16SRNA as well as 18SRNA data analysis, in which the only difference is the the use of silva database only when doing 18SRNA. However, now that I am doing ITS data, i understand that i need to print out a table for each 3 phylum and carry 3 different analysis. My only problem is that I am new to mothur and do not quiet understand where to change the mothur commands to print out the 3 different tables. Any help in that regard will be appreciated.

Thank you,

Roxy

you can use the UNITE2 database which is already formatted correctly here https://mothur.org/wiki/unite_its_database/

Thanks Kendra! so basically the difference between these three data types is the database we use for the alignment?
16S:greengenes, SILVA, RDP
18S:SILVA
ITS:UNITE2
let em know if that corrects. Thanks again!

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