BIOM Table

42 views
Skip to first unread message

dsan...@uic.edu

unread,
Mar 7, 2018, 5:26:54 PM3/7/18
to Qiime 1 Forum
Hi All, 

I am an Undergraduate Student at the University of Illinois at Chicago currently working with 16s rRNA data. I have realized my biom table does not display any taxa. Any ideas why this might be happening? I have attached my biom table.

Best,
Dolores Sanchez 
otu_table.biom

TonyWalters

unread,
Mar 7, 2018, 5:34:50 PM3/7/18
to Qiime 1 Forum
Hello Dolores,

what was the command you used to generate this table? Were there other .biom files created from the command you ran (depending on the command, you may have files with w_tax or something similar, indicating the OTU table with taxa in it).

-Tony

dsan...@uic.edu

unread,
Mar 7, 2018, 6:32:43 PM3/7/18
to Qiime 1 Forum
This is the first command I ran to create the OTU table 

make_otu_table.py –i combined_seqs_otus.txt –t rep_set_tax_assignments.txt –o raw_otu_table.biom


Then I ran a command to filter singletons and doubletons 

filter_otus_from_otu_table.py -i raw_otu_table.biom -o out_table_temp.biom -n 3

filter_otus_from_otu_table.py -i otu_table_temp.biom -o out_table.biom –-min_count_fraction 0.00005



- Dolores Sanchez 

TonyWalters

unread,
Mar 8, 2018, 5:49:37 AM3/8/18
to Qiime 1 Forum
Hello Dolores,

Those two filtering commands should not have altered the taxonomy. Maybe there are differences in the OTU ids in the combined_seqs_otus.txt and rep_set_tax_assignments.txt files? Can you see check if these IDs (should be first column in both files) look similar? It looked like all of the OTUs in your previously attached OTU table were denovo IDs-could you see if those show up in your rep_set_tax_assignments.txt file too (might be easiest to see them by converted to tab delimited first with command like this: biom convert -i table.biom -o table.from_biom.txt --to-tsv)?
Reply all
Reply to author
Forward
0 new messages