Hi Qiime2 experts!
I am currently running the deblur denoise-16S process and I'm having difficulty understanding the information in the stats.csv file.
The stats.csv file provides the following data:
I decided to sum up the following values: "reads-derep" + "reads-deblur" + "reads-hit-artifact" + "reads-chimeric" + "reads-hit-reference" + "reads-missed-reference," and it totaled 169,540 reads. Given that my "reads-raw" count was 183,787, I'm wondering if there are 14,247 reads missing. Am I correct?
If you open the deblur-stats.qvz visualization artifact, you can actually hover over the column headers which will display the definition of each.
Can you have a look through those first and let us know if you still have any outstanding questions?
Overall, the easiest way to understand what is happening to your reads is to go from left to right, each column corresponds to a step during the "deblur" process in sequential order. Sounds like to me you are losing a good portion of your reads before you actually start the "denoising" step of Deblur.