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new how-to guide: generate the tsv file that is accessed from the taxonomy barplots #4

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gregcaporaso opened this issue Feb 28, 2025 · 0 comments

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@gregcaporaso
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People tend to download the tsv file from taxa barplot and build other things based on it. Since it's in a viz, that format or the existence of the file, isn't guaranteed. So we should have a brief how-to that illustrates the following steps:

qiime taxa collapse --i-table table.qza --i-taxonomy taxonomy.qza --p-level 7 --o-collapsed-table species-table.qza

# you may have to rename the first column header in sample-metadata.tsv be "id" (rather than "sample-id") for this step to work
qiime metadata merge --m-metadata1-file species-table.qza --m-metadata2-file sample-metadata.tsv --o-merged-metadata species-table-w-metadata.qza

qiime tools export --input-path species-table-w-metadata.qza --output-path species-table-w-metadata
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