OTUtable标准化方法是什么

这篇文章主要介绍"OTUtable标准化方法是什么"，在日常操作中，相信很多人在OTUtable标准化方法是什么问题上存在疑惑，小编查阅了各式资料，整理出简单好用的操作方法，希望对大家解答"OTUtable标准化方法是什么"的疑惑有所帮助！接下来，请跟着小编一起来学习吧！

OTUtable标准方法

1.抽平方法：

single_rarefaction.py -i pick_de_novo_otus/otu_table_clean.biom -o pick_de_novo_otus/otu_table_clean_rare.biom -d 2032

2.css方法或者deseq2方法

normalize_table.py -i otu_table_clean.biom -a CSS -o otu_table_clean_css.biomnormalize_table.py -i otu_table_clean.biom -a DESeq2 -z -o otu_table_clean_deseq2_norm_no_negatives.biom

标准化之后数据处理：

################################################################################对OTU丰度进行标准化CSS方法 ：https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4010126/  http://qiime.org/scripts/normalize_table.htmlmkdir normalized_otu_css/normalize_table.py -i $workdir/5.pick_otu/pick_de_novo_otus/otu_table_clean.biom -a CSS -o normalized_otu_css/CSS_normalized_otu_table.biombiom convert -i  normalized_otu_css/CSS_normalized_otu_table.biom -o  normalized_otu_css/CSS_normalized_otu_table1.txt --to-tsv --header-key taxonomy#去掉只有界注释的OTUgrep -v 'k; _; _; B; a; c; t; e; r; i; a'  normalized_otu_css/CSS_normalized_otu_table1.txt >normalized_otu_css/CSS_normalized_otu_table.txt#注意biom格式转变 json to hdf5  ：https://www..com/article/1314biom convert -i normalized_otu_css/CSS_normalized_otu_table.txt -o  normalized_otu_css/CSS_normalized_otu_table_hdf5.biom --table-type="OTU table" --to-hdf5  --process-obs-metadata taxonomybiom summarize-table -i normalized_otu_css/CSS_normalized_otu_table_hdf5.biom -o normalized_otu_css/CSS_normalized_otu_table_summary.txt#对OTU丰度进行标准化 相对丰度echo Summarize taxaecho summarize_taxa:level 2,3,4,5,6,7 >taxa_summary_parm.txtecho plot_taxa_summary:x_width 8 >>taxa_summary_parm.txtecho plot_taxa_summary:bar_width 0.5 >>taxa_summary_parm.txtecho plot_taxa_summary:chart_type bar >>taxa_summary_parm.txtsummarize_taxa.py -i normalized_otu_css/CSS_normalized_otu_table_hdf5.biom -o normalized_otu_css/absolute_abundance -a --level 2,3,4,5,6,7summarize_taxa.py -i normalized_otu_css/CSS_normalized_otu_table_hdf5.biom -o normalized_otu_css/relative_abundance  --level 2,3,4,5,6,7mkdir normalized_otu_css/group_otus_cssfor i in  city loc country;do collapse_samples.py -b normalized_otu_css/CSS_normalized_otu_table_hdf5.biom -m $fastmap --collapse_fields $i --output_mapping_fp normalized_otu_css/group_otus_css/group.$i.txt --output_biom_fp normalized_otu_css/group_otus_css/otu_table_$i.biombiom convert -i normalized_otu_css/group_otus_css/otu_table_$i.biom -o normalized_otu_css/group_otus_css/otu_table_${i}.txt --to-tsv --header-key taxonomysummarize_taxa.py -i normalized_otu_css/group_otus_css/otu_table_$i.biom -o normalized_otu_css/group_otus_css/taxa_summary_relative.${i} -L 2,3,4,5,6,7summarize_taxa.py -i normalized_otu_css/group_otus_css/otu_table_$i.biom -o normalized_otu_css/group_otus_css/taxa_summary_absolute.${i} -a -L 2,3,4,5,6,7done

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