不同组间丰度差异比较
使用ANCOM差异丰度分析docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime feature-table filter-samples \
--i-table table.qza \
--m-metadata-file sample-metadata.tsv \
--p-where '='"'"'gut'"'"'' \
--o-filtered-table gut-table.qza
docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime composition add-pseudocount \
--i-table gut-table.qza \
--o-composition-table comp-gut-table.qza查看两个人肠道的差异对比
docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime composition ancom \
--i-table comp-gut-table.qza \
--m-metadata-file sample-metadata.tsv \
--m-metadata-column subject \
--o-visualization ancom-subject.qzv找到差异后进行物种分类
docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime taxa collapse \
--i-table gut-table.qza \
--i-taxonomy taxonomy.qza \
--p-level 6 \
--o-collapsed-table gut-table-l6.qza
docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime composition add-pseudocount \
--i-table gut-table-l6.qza \
--o-composition-table comp-gut-table-l6.qza
docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime composition ancom \
--i-table comp-gut-table-l6.qza \
--m-metadata-file sample-metadata.tsv \
--m-metadata-column subject \
--o-visualization l6-ancom-subject.qzv
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