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

38 views
Skip to first unread message

Jay T

unread,
Mar 6, 2017, 5:30:42 PM3/6/17
to Qiime 1 Forum
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

unread,
Mar 6, 2017, 10:46:33 PM3/6/17
to Qiime 1 Forum
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

unread,
Mar 7, 2017, 12:08:27 AM3/7/17
to qiime...@googlegroups.com
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

unread,
Mar 7, 2017, 11:31:06 AM3/7/17
to Qiime 1 Forum
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 
Reply all
Reply to author
Forward
0 new messages