不同组间丰度差异比较

生信喵

使用ANCOM差异丰度分析

1. docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime feature-table filter-samples \
   
2.   --i-table table.qza \
   
3.   --m-metadata-file sample-metadata.tsv \
   
4.   --p-where '[body-site]='"'"'gut'"'"'' \
   
5.   --o-filtered-table gut-table.qza
   
6. 
   
7. docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime composition add-pseudocount \
   
8.   --i-table gut-table.qza \
   
9.   --o-composition-table comp-gut-table.qza

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查看两个人肠道的差异对比

1. docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime composition ancom \
   
2.   --i-table comp-gut-table.qza \
   
3.   --m-metadata-file sample-metadata.tsv \
   
4.   --m-metadata-column subject \
   
5.   --o-visualization ancom-subject.qzv

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找到差异后进行物种分类

1. docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime taxa collapse \
   
2.   --i-table gut-table.qza \
   
3.   --i-taxonomy taxonomy.qza \
   
4.   --p-level 6 \
   
5.   --o-collapsed-table gut-table-l6.qza
   
6. 
   
7. docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime composition add-pseudocount \
   
8.   --i-table gut-table-l6.qza \
   
9.   --o-composition-table comp-gut-table-l6.qza
   
10. 
    
11. docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime composition ancom \
    
12.   --i-table comp-gut-table-l6.qza \
    
13.   --m-metadata-file sample-metadata.tsv \
    
14.   --m-metadata-column subject \
    
15.   --o-visualization l6-ancom-subject.qzv

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