normalize_by_copy_number.py – Normalize an OTU table by marker gene copy number¶
Description:
Usage: normalize_by_copy_number.py [options]
Input Arguments:
Note
[REQUIRED]
- -i, --input_otu_fp
- The input otu table filepath in biom format
- -o, --output_otu_fp
- The output otu table filepath in biom format
[OPTIONAL]
- -g, --gg_version
- Version of GreenGenes that was used for OTU picking. Valid choices are: 13_5, 18may2012 [default: 13_5]
- -c, --input_count_fp
- Precalculated input marker gene copy number predictions on per otu basis in biom format (can be gzipped).Note: using this option overrides –gg_version. [default: None]
- --metadata_identifer
- Identifier for copy number entry as observation metadata [default: CopyNumber]
- --load_precalc_file_in_biom
- Instead of loading the precalculated file in tab-delimited format (with otu ids as row ids and traits as columns) load the data in biom format (with otu as SampleIds and traits as ObservationIds) [default: False]
Output:
A normalized OTU table
Normalize the OTU abundances for a given OTU table picked against the newest version of Greengenes:
normalize_by_copy_number.py -i closed_picked_otus.biom -o normalized_otus.biom
Change the version of Greengenes used for OTU picking:
normalize_by_copy_number.py -g 18may2012 -i closed_picked_otus.biom -o normalized_otus.biom