Hi everyone,
I have just finished going through my qiime2 analysis following the moving pictures and fecal sample tutorial (for merging). I have created my phyloseq object using the following R code:
physeq_21<- qza_to_phyloseq(
features= "qiime2_exported/qza/merged_table.qza",
tree = "qiime2_exported/qza/merged-rooted-tree.qza",
taxonomy = "qiime2_exported/qza/silva-138.2-ssu-nr99-515f-806r-classified-taxonomy.qza",
metadata = 'qiime2_exported/tsvs/specified_metadata_21.tsv'
)
Now I need to remove Mitochondria from my taxonomy, I found that my lab peers used this code:
physeq21_nomitochondria <- subset_taxa(physeq_21, Family != "D_4__Mitochondria")
The thing is, when I run this code I get False:
"D_4__Mitochondria" %in% tax_table(physeq_21)[, "Family"]
Also when I run this code I get 300 more taxonomy classifications removed than when using just D_4__
and same for Chloroplast, I get 0 when using D_3__
but 100 when using Chloroplast.
For my classification I followed this tutorial using 138.2 silva database, LCA method.
I hope this helps, I just need to understand why:
- The code of D_4__ still removes samples even though it shows FALSE when looking for Mitochondria.
- Is it correct to use just Mitochondria and Chloroplast / and D_4__ for complete clean up?
Thank you for your time.