4.3.3 qiime2序列质控和feature表构建

Feature表和代表性序列生成

dada2去质控和去冗余,本实验有两批独立的数据,需要处理两次,生成代表序列和OTU表

qiime dada2 denoise-single
–p-trim-left 13
–p-trunc-len 150
–i-demultiplexed-seqs fmt-tutorial-demux-1.qza
–o-representative-sequences rep-seqs-1.qza
–o-table table-1.qza

qiime dada2 denoise-single
–p-trim-left 13
–p-trunc-len 150
–i-demultiplexed-seqs fmt-tutorial-demux-2.qza
–o-representative-sequences rep-seqs-2.qza
–o-table table-2.qza

合并不同组的序列和表

合并两组数据和OTU表

qiime feature-table merge
–i-table1 table-1.qza
–i-table2 table-2.qza
–o-merged-table table.qza

合并两组数据的代表性序列

qiime feature-table merge-seq-data
–i-data1 rep-seqs-1.qza
–i-data2 rep-seqs-2.qza
–o-merged-data rep-seqs.qza

OTU表统计

qiime feature-table summarize
–i-table table.qza
–o-visualization table.qzv
–m-sample-metadata-file sample-metadata.tsv

查看Feature/OTU表的统计结果

qiime tools view table.qzv

代表性序列统计

qiime feature-table tabulate-seqs
–i-data rep-seqs.qza
–o-visualization rep-seqs.qzv

查看代表性序列的统计结果

qiime tools view rep-seqs.qzv table.qzv文件中Feature/OTU表统计的结果如下,或在线查看详细信息:https://view.qiime2.org/visualization/?type=html&src=https%3A%2F%2Fdocs.qiime2.org%2F2017.6%2Fdata%2Ftutorials%2Ffmt%2Ftable.qzv

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