Taxa plots shows all samples


#1

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?


(Matthew Ryan Dillon) #2

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:


#3

Hi,

It’s QIIME2/2018.8.


#4

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.


(Nicholas Bokulich) #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:


#6

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


(Nicholas Bokulich) #7

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 — could you please share your dada2 stats results?


#8

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 look at the last number under non-chimeric to see how many reads are left?

v3v5-20181012-stats-dada2-s.qzv (1.2 MB)


(Nicholas Bokulich) #9

That is correct. The filtering steps read from left to right in that visualization, so chimera filtering is the last step and that number will tell you how many reads were retained in each sample after filtering. It looks like only one sample had all reads filtered, and I do not see that sample in the barplot: BRH1480294