I am using QIIME2-2019.4 version installed with conda.
I am having issues interpreting the results from the following command:
qiime feature-table merge \ --p-overlap-method sum \ --i-tables run_1_table-dada2.qza \ --i-tables run_2_table-dada2.qza \ --o-merged-table merged_runs_table-dada2.qza
Run 2 contains the samples that were sequenced in run 1 and some new samples that were missed in run 1. Therefore samples that are in both runs were called the same.
Run 1 has 95 samples and run 2 has 64 samples with a total of 111 unique samples.
I wanted to check that the output was correct so I ran:
qiime feature-table summarize --i-table merged_run_table-dada2.qza --o-visualization merged_run_table-dada2.qzv
Initially it looked fine with 111 samples.
The bit that confuses me is:
The merged sample table has a total frequency of 17,711,692
The Run 1 table has a total frequency of 123,450
The Run 2 table has a total frequency of 7,844,500
Additionally the feature counts for each sample in the interactive sample detail section is confusing me.
In the Merged table there are Five samples with a feature count of 0
In Run 1 table there are three samples with a feature count of 0 (only 1 of these samples overlaps with the 0 feature count samples in the merged run table).
In the Run 2 table there are Zero samples with a feature count of 0.
Any help with how the command works or if there is an issue here would be greatly appreciated.
If you have any other questions please don’t hesitate to reply.
Thanks for reading