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biocore / songbird

Vanilla regression methods for microbiome differential abundance analysis
BSD 3-Clause "New" or "Revised" License
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Songbird Input format #157

Closed y3zhu closed 1 year ago

y3zhu commented 2 years ago

Hi there,

I have my OTU tables in just .txt, .xlsx, or .csv format. I see that Songbird requires a .biom format. Are there any ways to work around this? Thank you

mortonjt commented 2 years ago

Yes. See biom format

https://biom-format.org/documentation/biom_conversion.html

On Fri, Feb 18, 2022 at 3:15 PM Yixin Zhu @.***> wrote:

Hi there,

I have my OTU tables in just .txt, .xlsx, or .csv format. I see that Songbird requires a .biom format. Are there any ways to work around this? Thank you

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pig-raffles commented 2 years ago

These comments on the Qiime forum can also help with getting the correct format for .txt input files prior to conversion to biom format

https://groups.google.com/g/qiime-forum/c/fcxKuJM3a6w https://groups.google.com/g/qiime-forum/c/EZC7VJ4t1ZI