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phinch won't load mothur-exported BIOM file #84

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stritttt opened this issue May 29, 2019 · 1 comment
Open

phinch won't load mothur-exported BIOM file #84

stritttt opened this issue May 29, 2019 · 1 comment

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@stritttt
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This is the output of the biom format using the mothur tool.
stability.opti_mcc.0.03.subsample.0.03.biom.gz

However, this was not suitable for the phinch input format.
So I fount a similar issue. (#48)
And I used the following two codes.
biom convert -i stability.opti_mcc.0.03.subsample.0. 03.biom -o file-for-phinch.biom --table-type="OTU table" --to-json
sed -i 's#null#{}#g' file-for-phinch.biom

But still phinch did not work.
So we changed null to [] as #82
But it still does not work.

@hollybik
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We've updated and revised the BIOM upload feature in the new Phinch desktop app. However, you also need to include taxonomy/ontology metadata and sample mapping information in the BIOM file that you upload into Phinch. Is that information in your current BIOM file?

I would recommend converting your mothur file outputs to tab-delimited format, and then using the BIOM conversion tools to combine this OTU table with your taxonomy data and sample mapping files.

Let me know if this works. If not, I can download your original file and look into this issue further.

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