qiime feature-classifier extract-reads --i-sequences 99_otus.qza --p-f-primer ACTCCTACGGGAGGCAGCAG --p-r-primer GGACTACHVGGGTWTCTAAT --p-n-jobs 4 --o-reads ref-seqs.qza 仅保留细菌的代表序列命令: qiime taxa filter-seqs --i-sequences ref-seqs.qza --i-taxonomy 99_otu_taxonom...
预先基于sklearn的物种注释分类器 extract-reads: 从参考中提取读取 fit-classifier-naive-bayes: 训练naive_bayes分类器 fit-classifier-sklearn: 训练几乎任意的scikit-learn分类器 vsearch-global: VSEARCH 全局对齐搜索 feature-table:用于按特征表处理样本 方法 filter-features: 从表中过滤特征 filter-features-condi...
qiime feature-classifierextract-reads\--i-sequences silva-138-ssu-nr99-seqs-derep-uniq.qza \--p-f-primer GTGYCAGCMGCCGCGGTAA \--p-r-primer GGACTACNVGGGTWTCTAAT \--p-n-jobs 2 \--p-read-orientation 'forward' \--o-reads silva-138-ssu-nr99-seqs-515f-806r.qza#合并重复 qiime r...
--o-classifier classifier.qza 下面就用训练好的分类器给自己的数据分类,然后是可视化,这里就不可视化了,基本就结束了。然后你得到taxonomy文件后就可以进行不同分类水平的菌属分析了。 qiime feature-classifier classify-sklearn \ --i-classifier classifier.qza \ --i-reads rep-seqs.qza \ --o-classificat...
qiime feature-classifier extract-reads \ --i-sequences 99_otus.qza \ --p-f-primerACTCCTACGGGAGGCAGCAG\ --p-r-primerGGACTACHVGGGTWTCTAAT\ --o-reads ref-seqs.qza # Train the classifier(分类器) # 基于筛选的指定区,生成实验特异的分类器 ...
time qiime feature-classifier extract-reads \ --i-sequences 85_otus.qza \ --p-f-primer GTGCCAGCMGCCGCGGTAA \ --p-r-primer GGACTACHVGGGTWTCTAAT \ --p-trunc-len 120 \ --p-min-length 100 \ --p-max-length 400 \ --o-reads ref-seqs.qza ...
time qiime tools import --type 'FeatureData[Taxonomy]' --input-format HeaderlessTSVTaxonomyFormat --input-path gg_13_8_otus/taxonomy/99_otu_taxonomy.txt --output-path ref-taxonomy.qza #指定V5-V7区训练器 time qiime feature-classifier extract-reads --i-sequences 99_otus.qza --p-f-primer...
#It has been shown that taxonomic classification accuracy of 16S rRNA gene sequences improves when a Naive Bayes classifier is trained on only the region of the target sequences that was sequenced (Werner et al., 2012). qiime feature-classifier extract-reads \ ...
qiime feature-classifier extract-reads \--i-sequencesref-seqs.qza \--p-f-primer ACTCCTACGGGAGGCAGCA \--p-r-primer GGACTACHVGGGTWTCTAAT \--p-trunc-len460\--p-min-length400\--p-max-length480\--o-readsref-seqs_v34.qza 虽然--p-trunc-len我们指定的是460,但是它会智能的根据引物来...
qiime feature-classifierextract-reads --i-sequences 99_otus.qza --p-f-primer ACTCCTACGGGAGGCAGCAG --p-r-primer GGACTACHVGGGTWTCTAAT --p-n-jobs 4 --o-reads ref-seqs.qza 仅保留细菌的代表序列命令: qiime taxafilter-seqs --i-sequencesref-seqs.qza ...