Hello, I am an attendee of qiime2 forum which was held in las vegas.
I have one question that “how do I know what has been removed during denoising step with dada2?”
Specifically, I wonder that the number of singletons because the taxanomy bar plot looks 100% but the 100% value is not including singletons so I think the 100% is not the real 100%.
In addition, I wonder that how do I know the number of chimera also.
Thank you for reading this question.
Best regards,
I'm not sure I understand the question correctly. The taxonomy bar plots will reflect your data after any quality-control step, so the 100% is only relative to the number of features observed in your feature-table. Is the question more with respect to whether dada2 filters out singleton reads?
Pinging @benjjneb on this, I know that the plugin doesn't report on it at this time.
Right now the number of chimeras is not reported out by the plugin. You can find that number by running your data again without chimera removal (--p-chimera_method none) and compare, but it would be nice to have that be more transparent without having to rerun the data.
There is a plan to break the current dada2 commands into more granular pieces (Split filtering into its own command? · Issue #51 · qiime2/q2-dada2 · GitHub) but it is on hold until Pipelines are implemented. Better reporting of the results of the filtering and chimera steps might make sense to add at that point.
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The DADA2 plugin in QIIME 2 2017.12 now prints how many reads were filtered, denoised, merged, and non-chimeric to stdout! (You can capture that via the --verbose flag.)