Verry small Biom file

[Camille1000 (Camille)]

Dear Qiime2 friends,

I am very new to this and a have a few questions

So i am doing 16s using oxford nanopore tech and i amplified the whole 1500bp region.
First do you have scripts recommendations?
I have one but i need an ASV table and i dnt have it yet but i manage to create a biom file.
My concern is that my biom file is very small compared to the amount of sequencing data i have as input. In this i have 15 files of 4000 sequences and when i do taxa-barplot-visualtisation i have much more than in the biom file. Do you have some suggestions?
Thankyou !!

Camille

[Nicholas_Bokulich]

Hi @Camille1000 ,

@Camille1000

First do you have scripts recommendations?

It is certainly possible to process nanopore 16S data entirely within QIIME 2. You would just use OTU clustering with q2-vsearch in place of denoising with q2-dada2 (which does not currently support ONT as far as I know), and otherwise you could follow the steps described in the various tutorials and use more or less all other QIIME 2 actions.

There is also a pipeline for ONT data that uses QIIME 2 called METONTIIME. I have not used it myself yet, but there is some discussion of it on the forum.

@Camille1000

My concern is that my biom file is very small compared to the amount of sequencing data i have as input. In this i have 15 files of 4000 sequences and when i do taxa-barplot-visualtisation i have much more than in the biom file. Do you have some suggestions?

Small in terms of file size or in terms of sequence count? Could you please share the QZVs of:

1. the barplot that you showed
2. run qiime feature-table summarize on the feautre table that you used to make the barplot and share the QZV here.

Thanks!

[Camille1000 (Camille)]

Hi Nicholas,

Thankyou for your answer !
Okay for the scripts i will check METONTIIME, thanks

My final file is very small in terms of different bacteria present in the sample so in sequence count.

And I also have an other question, what does this table mean?
stats(1).qzv (1.9 MB)

Here are the two qzv,
If there is more info needed please let me know,
Thanks again !

Camille
id-filtered-table_clean(1).qzv (1.1 MB)

taxa-barplots-clean(1).qzv (827.2 KB)

[Nicholas_Bokulich]

Hi @Camille1000 ,

@Camille1000

My final file is very small in terms of different bacteria present in the sample so in sequence count.

Okay I see what you mean now. How are you viewing the biom file? It appears cut off, as indeed you have more taxa observed in the barplot.

How are you exporting your feature table to biom? When converting to CSV, how many lines does the CSV have?

[Camille1000 (Camille)]

Hi,

I convert to tsv, and i have 22lines
I will try to csv maybe?
I use this command :

biom convert -i taxo/taxa-table-level6-filtered/feature-table.biom -o taxo/taxa-table-level6-filtered/DNA-16S-table-level6-filtered.tsv --to-tsv

Thanks !

[Camille1000 (Camille)]

Hi, still the same if i do tsv or csv...
I dont understand 7

Update :

I had a filtration step after that, so when i dont do it i have a large file !!
Thankyou @Nicholas_Bokulich for your help !

[Nicholas_Bokulich]

@Camille1000

I had a filtration step after that, so when i dont do it i have a large file !!
Thankyou @Nicholas_Bokulich for your help !

Thanks for clarifying! Okay indeed that explains it.

Good luck with the next steps!