How to change taxa name in .biom file?

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Alex Vante

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May 11, 2020, 5:45:57 AM5/11/20
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Dear users,
I am currently facing a small problem with taxonomy assignments of certain OTUs.
I have run QIIME 1 on amplicon sequencing data, and performed de novo OTU picking using 97% identity threshold, and subsequently assigned taxonomy using greengenes_release/gg_13_8_otus version.
I was puzzled about the assinment of OTUs to the species Streptococcus alactolyiticus, thus I have recovered the corresponding OTUs and performed BLASTn search, revealing that most of the OTUs actually belong to the species S. thermophilus, which is consistent with the analysed sample.
Is there a way to correct the taxonomic assignment in .biom file?
Thank you in advance for your kind reply.

TonyWalters

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May 11, 2020, 6:00:18 AM5/11/20
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Hello Alex,

First the caveat that QIIME 1 isn't updated any longer, and the 2013 Greengenes reference data is getting dated. See QIIME 2 (SILVA is the commonly used reference dataset for ribosomal SSU genes, and is much more frequently updated): https://qiime2.org/

For your particular question, you could convert the OTU table from biom to tab-delimited format, following the examples here: https://biom-format.org/documentation/biom_conversion.html#special-case-usage-examples

It may be simpler from a 'citing your approach' method, to keep the OTU as is, and just clarify in the manuscript that the 2013 reference database assigned the OTU as X, but the current NR database was a better (and unambiguous?) match to Y.
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