Summary statistics after dada2 questions

[thermokarst]

@MMC_northS

Using dada I cannot know exactly the result because it has not statistics of the command (like deblur). I saw that with verbose I can see in the screen more or less that statistic but only appeared for me in 6 samples (21 in total) and I do not know why. When I convert to vizualizer the table from dada, the file say that I have 21 samples (which is correct) so I do not know why the statistics only appear for 6 samples. Any idea??

Hi @MMC_northS - I don't entirely follow your whole post here, but for this section, does this answer your question?

Dada2 not picking up all samples in artifact?

Hi @zackljones and @Mehrbod_Estaki, The reason for this is that there is a parameter --p-n-reads-learn which is the number of reads to use to estimate the error model. By default this is set to 1,000,000 and once it has acquired that many reads, it stops looking for more. In practice this means you will see it run through a couple (or even most) of your samples before it has captured enough reads. Although I've seen this step completed in as few as 2 samples for very large datasets.

Please let us know if that answers your question!

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@MMC_northS

With Deblur my data are not bad at all but the trimming limits so much my analyses, because if I not use very short fragment I loss many sequences about the trimming.

@MMC_northS

Any other option for doing the feature table without trimming??

These seem to be unrelated to your question above - can you please post as a new, separate question here on the forum? Thanks!