how to know the ASV for individual samples from the results of DADA2 denoise process

User Support
#1

Hi all,

I am analyzing the sequences of mcrA, which is related to methanogenesis in prokaryotes, obtained through MiSeqs from environmental samples.

I have successfully gotten three output files of DADA2, in terms of feature table, rep-seqs, and states.
I would like to see the distribution of ASVs per each sample, but the feature_table showed the total number but not the number in each sample.

Do somebody know if there is any way to see what I would like to see?

Hee-Sung

3 Likes
#3
#7

Hi @baehsung,

The feature-table.qza is storing a BIOM table in it which is exactly what you are looking for, as it can be read as a samples by ASV table. I'm guessing when you say it only showed total numbers you are referring to the output of feature-table summarize which is intended to give you a summary of the feature-table, rather than the actual table itself. If you want to see the actual table you can feed your feature-table into qiime metadata tabulate and that will give you a visualization with the actual frequencies per sample.

Hope that helps.

2 Likes
#8

Thanks Estaki,

Now I got exact one along to your advice !!

Hee-Sung

1 Like
#9
#10

Hi @baehsung

You can also create a ASV bar-plot follow this post

1 Like
#11

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.