qiime1 taxonomy assignment
0
0
Entering edit mode
5.2 years ago
Bioinfonext ▴ 460

I need to ask one thing about qiime1 for OTU assignment I used below command is it correct to use -m rdp when providing fasta and taxonomy file

I assign OTU using this command:

assign_taxonomy.py -i seqs.fna_rep_set.fasta –r 97_otus.fasta –t 97_otu_taxonomy.txt -m rdp

I used fasta and taxonomy file from latest greengenes database gg_13_8_otus.tar.gz

I am not sure -m rdp is correct to use here?

Thanks

next-gen • 1.2k views
ADD COMMENT
0
Entering edit mode

Thanks, it is resolved. by default, it used uclust method and I have provided rdp method.

ADD REPLY

Login before adding your answer.

Traffic: 1913 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6