Hi, Even though I filtered my sequences using dada2 and some samples were lost, when I use that table to get my taxa plot, still all the samples are there. How is that possible?

What version of QIIME 2 are you running? Can you provide your barplot QZV so that we can see an example of what you are describing (also, we can then look at the provenance)? Thanks! :t_rex: :qiime2:

Also, most of my human and marmoset samples taxa are either unidentified or identified at the kingdom level only. I tried training the classifier based on primers and it got even worse.

Thank you for sharing the QZV [image] Negin: Even though I filtered my sequences using dada2 and some samples were lost, when I use that table to get my taxa plot, still all the samples are there. How is that possible? The provenance for that barplot indicates that you are using an unfiltere…

unfiltered? hmm I don't think so because the table, rep-seq and everything I got is after the filtering step.

[image] Negin: unfiltered? hmm I don’t think so because the table, rep-seq and everything I got is after the filtering step. I only mean that you did not explicitly remove these samples with qiime feature-table filter-samples. I understand that some samples had all reads filtered out by dada2…

You're right. For some reason, I thought my water samples were removed but they were not removed completely. One of them had only one read left after all the filtering steps. So based on this stats, does it mean that for example, after all the filtering steps, NC2 has still one read left? Should I l…

[image] Negin: So based on this stats, does it mean that for example, after all the filtering steps, NC2 has still one read left? Should I look at the last number under non-chimeric to see how many reads are left? That is correct. The filtering steps read from left to right in that visualizat…

Hi Nicholas, Thanks for your reply. Just another quick related question. When I run beta diversity analysis and get the emperor plots, I have only one marmoset sample left even though the dada2 filtered data does not show that any of the samples are removed. When I want to compare beta-diversity, i…

[image] Negin: When I run beta diversity analysis and get the emperor plots, I have only one marmoset sample left even though the dada2 filtered data does not show that any of the samples are removed. This is because the "core-metrics" action you are using performs even rarefaction prior to c…

Taxa plots shows all samples

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Nicholas_Bokulich (Nicholas Bokulich) December 17, 2018, 3:44pm 5

Thank you for sharing the QZV

The provenance for that barplot indicates that you are using an unfiltered table as input — is it possible you mixed up the files?

It looks like you opened up this topic, so this question will be answered there: