qiime1进行多样性分析

1.beta 多样性分析

1）随机抽样参数设定

biom summarize-table -i otu_table_handle/otu_table_mc2.biom

图1

去除包含过多或过少的 OTU tag ，在这里我选最小为40205

filter_samples_from_otu_table.py -i otu_table_handle/otu_table_mc2.biom -o otu_table_handle/filter.biom -n 40205

2）使用single_rarefaction.py进行随机抽样（抽平操作）

single_rarefaction.py -i otu_table_handle/otu_table_mc2.biom -o otu_table_handle/otu_table_mc2_even40205.biom -d 40205

查看抽平后的 OTU table

biom summarize-table -i otu_table_handle/otu_table_mc2_even40205.biom

图2

3）beta 多样性分析脚本-beta_diversity.py

mkdir beta_diversity

beta_diversity.py -i otu_table_handle/otu_table_mc2_even40205.biom -o beta_diversity/beta_div --metrics weighted_unifrac,unweighted_unifrac -t phylogeny/rep_set.tre

4）beta 多样性分析脚本-principal_coordinates.py

principal_coordinates.py -i beta_diversity/beta_div/ -o beta_diversity/beta_result

5）beta 多样性分析脚本-make_2d_plots.py

make_2d_plots.py -i beta_diversity/beta_result/pcoa_weighted_unifrac_otu_table_mc2_even40205.txt -o beta_diversity/bdiv_2d_wu -m mapping.txt

make_2d_plots.py -i beta_diversity/beta_result/pcoa_unweighted_unifrac_otu_table_mc2_even40205.txt -o beta_diversity/bdiv_2d_uu -m mapping.txt

6）beta 多样性分析脚本-make_emperor.py 

make_emperor.py -i beta_diversity/beta_result/pcoa_weighted_unifrac_otu_table_mc2_even40205.txt -o beta_diversity/bdiv_3d_wu -m mapping.txt

make_emperor.py -i beta_diversity/beta_result/pcoa_unweighted_unifrac_otu_table_mc2_even40205.txt -o beta_diversity/bdiv_3d_uu -m mapping.txt

2.alpha 多样性分析

1）使用 multiple_rarefaction.py 进行随机抽样

这里我设定从最小10开始，最大67053，步长为1340

mkdir alpha_diversity

multiple_rarefactions.py -i otu_table_handle/otu_table_mc2.biom -m 10 -x 67053 -s 1340 -o alpha_diversity/rarefactions

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2）alpha 多样性分析脚本-alpha_diversity.py

alpha_diversity.py -i alpha_diversity/rarefactions -o alpha_diversity/alpha_div --metrics observed_species,chao1,shannon,simpson -t phylogeny/rep_set.tre

3）alpha 多样性分析脚本-collate_alpha.py

collate_alpha.py -i alpha_diversity/alpha_div -o alpha_diversity/alpha_collate

4）alpha 多样性分析脚本-make_rarefaction_plots.py

make_rarefaction_plots.py -i alpha_diversity/alpha_collate -o alpha_diversity/alpha_plot -m mapping.txt

3.Rank-Abundance 曲线

mkdir rank_abundance

plot_rank_abundance_graph.py -i otu_table_handle/otu_table_mc2.biom -s '*' -x -o rank_abundance/rank_abundance.pdf -n