Hi,
how can obtain summary statistics after denoising and quality filtering with DADA2?
Thank you!
Hi @iptz1! I’m not sure what sort of summary statistics you’re looking for, but check out qiime feature-table summarize – that’ll probably get you what you’re looking for. This section of the Moving Pictures tutorial has examples.
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Hi @jairideout and thank you for your help! I was looking for something like qiime quality-filter visualize-stats or qiime deblur visualize-stats available for Deblur, but for DADA2. Do you have any suggestions?
Thank you!
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Unfortunately we don’t have a visualizer for DADA2 stats yet. There is an open issue to add this feature, and there’s a few ideas being tossed around in that thread for how to solve it. I don’t have a specific ETA on when the feature will be available in a release – it may happen in the 2017.12 release or early next year. We’ll follow up here when the feature is available in a release!
In the meantime, you could try running your DADA2 commands with the --verbose flag to see some info being output by DADA2 as it is running. The output is currently pretty limited though, so it may not give you the stats that you’re looking for.
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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.)