EMP Biom Files

Not too sure what to do with .biom files from S.Gibbons

Two files:

full_emp_table_w_tax_closedref.biom
full_emp_table_w_tax.biom

Need to figure out how to pull Curtobacterium metadata from above master files

***Neither attempt has been able to utilize the open reference .biom file - ERROR***

Attempt 1:

• QIIME - filter_samples_from_otu_table.py
• Under "List-based Filtering":
• -i full_emp_table_w_tax_closedref.biom
• --sample_id_fp curto-only.txt
• RESULT: nothing
• PROBLEM: curto-only.txt contains OTUs, not individual samples

Attempt 2:

• QIIME - filter_otus_from_otus_table.py
• Use feature to extract Curtobacterium OTUs
• -i full_emp_table_w_tax_closedref.biom
• -e curto.only.txt #this excludes samples from new .biom
• --negate_ids_to_exclude 
• RESULT: generates new .biom file
• PROBLEM: I think it only contains a handful of OTUs, or not working?
• Summary table from .biom
• Num samples: 15481
• Num observations: 2
• Total count: 197
• Table density (fraction of non-zero values): 0.005
• Compared to Summary table from master .biom
• Num samples: 15481
• Num observations: 69444
• Total count: 654448644
• Table density (fraction of non-zero values): 0.016
• Generated by "biom summarize-table" function