Running diversity analyses on deblurred sequences in Qiime 1.91...?

[Jay T]

I tried running the core_diversity_analyses.py script in qiime using the deblurred sequences and the CD analyses script said I didn't have metadata in my biom file. When I added the metadata it still did not run properly. I understand deblur is integrated into Qiime 2 but I was wondering if anyone have completed their diversity analyses using Qiime. If so can someone steer me into right direction, I would be greatly appreciative. 

Thanks,

JT

[jonsan]

Hi Jay, 

What exact command are you executing? It should look something like the one below, from the scripts documentation page:

core_diversity_analyses.py -i $PWD/otu_table.biom -o $PWD/core_output -m $PWD/map.txt -t $PWD/rep_set.tre -e 1000

You shouldn't need any metadata in the biom file itself, as you can provide a metadata mapping file separately. 

What error messages are you seeing?

cheers,

-jon

[Jay T]

The problem is that the OTU IDs within the deblur biom file aren't actual taxa. They are sequences. So I used assigned_taxonomy.py on the deblurred sequence hits. I now have a taxonomy file that has the greengenes taxonomic ids and the corresponding sequences. I'm an unsure however how to get this data back into the OTU table. 

[jonsan]

Hi Jay, 

Ah, I see. You'll want to use the following command, taken from the bottom of a documentation page on the biom project site:

biom add-metadata -i deblurred_table.biom -o deblurred_table_withtax.biom --observation-metadata-fp assign_taxonomy_output.txt --observation-header OTUID,taxonomy,confidence --sc-separated taxonomy --float-fields confidence

Let me know if that works for you!

-j