Unclassified, Eukaryote data in Dada2 for ASV.

,
1

Hi Everyone,
I have used DADA2 for generating ASV files following tutorial.Hands-on: Building an amplicon sequence variant (ASV) table from 16S data using DADA2 / Building an amplicon sequence variant (ASV) table from 16S data using DADA2 / Microbiome
Its works good, generates ASV files, but upon using PhyloseqR visualization tool, it displays unclassified, Eukaryota, Archae kingdoms data, there is no option for removing lineage to get exact data.
Is there any way to remove the unwanted lineage from the data, so that only bacterial species will be displayed in abundance bar plots.

Thanks,
Shweta

2

Hi @Shweta.203

Iā€™m going to bring in some of the people who created these tutorials and know the workflows best. They may reply here or there, and definitely feel free to join the chat. ā†’ You're invited to talk on Matrix

The link to the Matrix chat is also at the very top of tutorial listing here, too, if you or anyone else ever needs to find it again. ā†’ Microbiome / Tutorial List

Hope this helps! :slight_smile:

3

Hi @Shweta.203;
there are multiple ways to remove unwanted lineages from the data.
But I am not sure if we have a very simple Galaxy tool available.
But I will look into adding one. For now you could use:
(a) the interactive phyloseq tool in Galaxy and apply a filter based on Kingdom and only choose Bacteria. See example figure

Selection_200
Selection_200602Ɨ338 16.4 KB

(b) If you actually need the phyloseq object, you could filter in R with:

# Load the phyloseq package
library(phyloseq)

# Assume `physeq` is your phyloseq object

# Check the taxonomy table to identify the rank "Family"
tax_table(physeq)

# Filter to keep only taxa where Family is "Bacteria"
physeq_bacteria <- prune_taxa(tax_table(physeq)[, "Family"] == "Bacteria", physeq)

# Check the resulting object
physeq_bacteria

You could do this in the interactive tool R-studio.
(c) You can also use the ampvis2 tool, it also supports filtering, you can then use ampvis2 for plotting, but cannot export the filtered object - need to add this tool as well.

Let me know if you need further help !

1 Like