Importing and exporting OTU abundance tables
It is possible to import a biom, a csv or an excel file as an OTU abundance table, by going to File | Import (
) | Standard Import... () and force the input as type "OTU abundance table (.xls, .xlsx, .csv)" or "Biom (.biom)". Currently supported versions for BIOM file format are versions 1.0 and 2.1.
This importer allows users to perform statistical analyses on abundance tables that were not generated by OTU clustering tool. Note that abundance tables that are imported will not contain metadata or grouping information, and thus metadata has to be re-applied using the Add Metadata to Abundance Table tool after import.
For example, Terminal Restriction Fragment Length Polymorphism (TRFLP) data can be imported and treated similarly as OTU abundance tables. However, all sequence-based actions cannot be applied to this data (i.e., multiple sequence alignment, tree reconstruction and phylogenetic tree measure estimation).
The importer recognizes the following column headers:
- Name The name of the OTU, specified by either the reference database or by the OTU representative.
- Taxonomy The taxonomy of the OTU, as specified by the reference database when a database entry was used as reference, e.g "Bacteria; Bacillota; Bacilli; Lactobacillales; Lactobacillaceae; Lactobacillus; Lactobacillus gasseri".
- Sequence The sequence of the centroid of the OTU.
- Any other header of a column with integer values: The header is interpreted as sample name and the values as abundance values. Values must be absolute counts and not relative abundances.
It is furthermore possible to export abundance tables to different formats, but it is recommended to use the Biological Observation Matrix (biom) file format (biom-format.org) as a standardized format. Currently, the only supported version for export is 2.1.
Sunbursts graphs can be exported in the following formats: *.jpg, *.tif, *.png, *.ps, *.eps, *.svg.