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BIOM microbial data format and file conversion method

2025-01-26 Update From: SLTechnology News&Howtos shulou NAV: SLTechnology News&Howtos > Development >

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This article mainly introduces "BIOM microbial data format and file conversion methods". In the daily operation, I believe that many people have doubts about BIOM microbial data format and file conversion methods. Xiaobian consulted all kinds of materials and sorted out simple and easy-to-use operation methods. I hope it will be helpful to answer the doubts about "BIOM microbial data format and file conversion methods". Next, please follow the editor to study!

BIOM is currently available in 1.0 JSON and 2.0 HDF5.

JSON is a format widely supported by programming languages, similar to hash key-value pair results. According to the degree of looseness of the data, different storage structures are selected to save space.

2.0 HDF5 is a binary format that is supported by many programming languages, making it more efficient to read and save space.

How to save storage:

Common commands for biom format conversion:

Convert classic table to HDF5 or JSON format

Biom convert-I table.txt-o table.from_txt_json.biom-- table-type= "OTU table"-- to-jsonbiom convert-I table.txt-o table.from_txt_hdf5.biom-- table-type= "OTU table"-to-hdf5

Convert biom to classic format

Biom convert-I table.biom-o table.from_biom.txt-- to-tsv

Convert biom to classic format and include species annotation information in the last column

Biom convert-I table.biom-o table.from_biom_w_taxonomy.txt-to-tsv-header-key taxonomy

Convert biom to classic format, include species annotation information in the last column, and rename it to ConsensusLineage

This feature is useful for column names that some software requires.

-biom convert-I table.biom-o table.from_biom_w_consensuslineage.txt-to-tsv-- header-key taxonomy-- output-metadata-id "ConsensusLineage"

Exchange of tables with species annotations

Biom convert-I table.biom-o table_tax.txt-- to-tsv-- header-key taxonomybiom convert-I table_tax.txt-o new_table.biom-- to-hdf5-- table-type= "OTU table"-- process-obs-metadata taxonomybiom convert-I table_tax.txt-o new_table.biom-- to-json-- table-type= "OTU table"-- process-obs-metadata taxonomy

Take subset subgroups for analysis

Biom subset-table-I otu_table.biom-a sample-s samples_list.txt-o otu_table_subset.biom

Samples_list.txt is the name of a single column sample.

Filtering method in biom file:

If qiime1 is installed in the system, there will be a script for filtering biom files, so it is convenient for us to filter our own numbers for subsequent analysis:

# filter by sample data sequencing quantity: select samples with counts > 30000 filter_samples_from_otu_table.py-I otu_table.biom-o otu_table1.biom-n 3000 cycles to view the filtering results: biom summarize-table-I otu_table1.biom# filter by sample data sequencing quantity: select counts

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