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OTU biom table

Get OTU count from .biom table

print_biom_table_summary.py   # old command

raw sequence counts

# Get number of OTU's per sample (not normalized OTU table)
biom summarize-table -i otu_table_mc2_w_tax.biom --qualitative -o stats_OTUs_per_sample.txt

# Get number of reads per sample (not normalized OTU table)
biom summarize-table -i otu_table_mc2_w_tax.biom -o stats_reads_per_sample.txt

head -20 stats_reads_per_samples.txt    # print top 20 lines
  Num samples: 40
  Num observations: 113869   (total number of OTU's)
  Total count:     1436372   (total number of sequences) 
  Table density (fraction of non-zero values): 0.041

  Counts/sample summary:
   Min:       5123.0
   Max:      51423.0
   Median:   22415.0
   Mean:     27632.043
   Std. dev.: 5203.534
   Sample Metadata Categories: None provided
   Observation Metadata Categories: taxonomy

  Counts/sample detail:
  SampleA: 5123.0
  SampleB: 5634.0
  SampleC: 6192.0
   °°°

http://biom-format.org/documentation/summarizing_biom_tables.html

Convert otu_table.biom to .tsv tab separated text file for using in Excel

# Convert .biom to .tsv text file (including taxa labels)
biom convert -i otu_table.biom -o otu_table.tsv --to-tsv --header-key taxonomy

# Convert .tsv text file to .biom file (requires column 'taxonomy')
biom convert -i otu_table.tsv -o otu_table.biom --table-type="OTU table" --process-obs-metadata taxonomy --to-hdf5

How to edit  .biom format files?

View biom-file on command line
biom head -i otu_table.biom


# example: remove all control samples from biom file  (keep all '*' , but not '!' Control)
filter_samples_from_otu_table.py -i otu_table.biom -o otu_table_without_Control.biom -m mapfile.txt -s 'Treatment:*,!Control'


Python package
http://biom-format.org/
R package
https://cran.r-project.org/web/packages/biom/



read more

Biom file format
http://biom-format.org/documentation/biom_format.html
http://biom-format.org/documentation/biom_conversion.html

OTU table and .biom format
http://www.wernerlab.org/teaching/qiime/overview/c

Subpages (1): QIIME: split OTU table