物种分类鉴定及可视化

生信喵

物种组成分析

1. wget \
   
2.   -O "gg-13-8-99-515-806-nb-classifier.qza" \
   
3.   "https://data.qiime2.org/2023.2/common/gg-13-8-99-515-806-nb-classifier.qza"
   
4. docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime feature-classifier classify-sklearn \
   
5.   --i-classifier gg-13-8-99-515-806-nb-classifier.qza \
   
6.   --i-reads rep-seqs.qza \
   
7.   --o-classification taxonomy.qza
   
8. #更换官网的注释库silva对比下结果
   
9. docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime feature-classifier classify-sklearn \
   
10.   --i-classifier silva-138-99-515-806-nb-classifier.qza \
    
11.   --i-reads rep-seqs.qza \
    
12.   --o-classification taxonomy_silva.qza
    
13. 
    
14. 
    
15. docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime metadata tabulate \
    
16.   --m-input-file taxonomy.qza \
    
17.   --o-visualization taxonomy.qzv
    
18. docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime metadata tabulate \
    
19.   --m-input-file taxonomy_silva.qza \
    
20.   --o-visualization taxonomy_silva.qzv
    
21. #下载到本地去view，结果相似。

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      物种分类完，画条形图

1. docker run -t -i -v $(pwd):/data quay.io/qiime2/core:2022.2 qiime taxa barplot \
   
2.   --i-table table.qza \
   
3.   --i-taxonomy taxonomy.qza \
   
4.   --m-metadata-file sample-metadata.tsv \
   
5.   --o-visualization taxa-bar-plots.qzv

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