How to convert merged_abundance-table into a biom file?

Question

[dpc]

Hi there!!! I have profile around 60 WGS metagenomic samples with MetaPhlAn 3.0. In the next step I have merged all the output profile files into merged_abundance_table with merge_metaphlan_tables.py function from MetaPhlAn 3.0.

1. Now, can anyone please tell me how can I convert this merged_abundance_table into a biom format? or,

2. How can I merge all the biom outputs obtained from each of the sample?

Thanks, DC7

Answer 1

[antonioggsousa]

Hi,

To merge one table into biom you can use biom-convert utilities: https://biom-format.org/documentation/biom_conversion.html

biom convert -i otu_table.txt -o new_otu_table.biom --to-hdf5 --table-type="OTU table" --process-obs-metadata taxonomy

Can you post just part of you table here in tsv format?

António

Answer 2

[D]

Hi,

If you use merge_metaphlan_tables.py the output will be expressed by relative abundances.

I encourage to you to use absolute abundance for phyloseq downstream analysis.

See the code created by timierg in https://forum.biobakery.org/t/merge-metaphlan-tables-py-with-absolute-abundance/1839

Kind regards,

Magí.