Help with picrust2 using Mothur

[Allan Amorim Santos]

Hi everyone, hope you are doing well.

I'm a beginner user and I'm working on Mothur for analysing my v4 sequencing data.

Following my experimental setup, we would like to predict the functions by using picrust2.

Basicaly, I was reading that I need fna file (conventional fasta file) and biom file; however I'm not sure how to proceed with biom file using Mothur.

After generating biom file following the commands, I found some errors in picrust2 since OTU/ASV id is not the same in fasta and biom.

Please, could anyone help me with this?

Thank you so much!! 

[Robyn Wright]

Hello,

I'm afraid that it's a while since I've used the Mothur pipeline myself, but essentially you need a fasta file that contains the representative sequences for your OTUs/ASVs as well as a feature table that contains the OTU/ASV names in the first column, and counts within your samples in the other columns. You can use either a biom or txt file for the count file. If you based your analyses on this MiSeq SOP, then it appears to me that you'd be looking to use the final shared file (probably final.count_table) and final.fasta. Otherwise, if you share the output files that you have then I may be able to identify which ones you should use.

Robyn