# Merged abundance table to biom format

**URL:** <https://forum.biobakery.org/t/merged-abundance-table-to-biom-format/728>\
**Category:** MetaPhlAn\
**Created:** [July 15, 2020, 10:00pm UTC](https://forum.biobakery.org/t/merged-abundance-table-to-biom-format/728 "2020-07-15T22:00:42Z")\
**Posts on this page:** 1\
**Showing post:** 6

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**Author:** ![D11](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/d11/32/1224_2.png) [@D11](https://forum.biobakery.org/u/D11)\
**Post date:** [March 11, 2022, 11:48am UTC](https://forum.biobakery.org/t/merged-abundance-table-to-biom-format/728/6 "2022-03-11T11:48:10Z")

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Hello researcher and developer @fbeghini.

It’s my first time to analyse shotgun and I have difficulties to communicate metaphlan output to phyloseq.

I have used `merge_metaphlan_tables.py` but in absolute counts (code available from [https://forum.biobakery.org/t/merge-metaphlan-tables-py-with-absolute-abundance/1839](https://forum.biobakery.org/t/merge-metaphlan-tables-py-with-absolute-abundance/1839)) but when I tried to construct the otu table I obtained the following output:

 ![imageoutput](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/7/74382e337bb3b50205f1da5409c2ab6335ee5c71.png)

I have all the taxonomic ranks mixed in the first column. Therefore, I understand that I cannot do tax\_glomf function in phyloseq R package.

Therefore it will be interesting to construct 7 independent OTU tables (one for each taxonomic rank) and construct 7 phyloseq objects?

Thanks for your help,

Kind regards,

Magí.

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