determine mean read depth

[Brian Simison]

Hello,

I have used the Microbiome_helper scripts and pipeline (Amplicon SOP v2 (qiime2 2020.8)) to analyze our microbiome data (16S). A reviewer has asked us for our final mean read depth. I have looked at my rarefaction data, summary tables, etc in QIIME 2 View and I have looked at my many .qzv files and I cannot find this information. 

Which analysis produces this info?

I hope to rewrite something like:

In total, 1,351 unique ASVs were observed, with a mean read depth of X sequences across 442 samples.

thank you,

[Brian Simison]

Does "Frequency per sample" mean read depth?

[Andre Comeau]

Yes, exactly. In QIIME2 speak, "features" are ASVs and then their "frequencies" are read depths...either for the ASVs themselves or for the samples. So that table is showing you the min/max/average read depths for your samples. Normally you would have also subsampled in step 8 to a certain number for the diversity calculations (so you can report both).

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From: microbio...@googlegroups.com <microbio...@googlegroups.com> on behalf of Brian Simison <wbs...@gmail.com>
Sent: Tuesday, March 15, 2022 6:09 PM
To: Microbiome Helper <microbio...@googlegroups.com>
Subject: [microbiome-helper] Re: determine mean read depth

 

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[Brian Simison]

Thank you so much!