taxonomy mitochondria vs D_4__Mitochondria

General Discussion
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1

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:

  1. The code of D_4__ still removes samples even though it shows FALSE when looking for Mitochondria.
  2. Is it correct to use just Mitochondria and Chloroplast / and D_4__ for complete clean up?

Thank you for your time.

2

Hi @saif_s,

It appears you are using a very old version of SILVA db parsers. The D_x__ schema has not been used in several years. You can remove that portion of the search term. We've moved to a more accurate Greengenes-like taxonomy. I'd recommend looking through the RESCRIPt tutorial on how to make your own SILVA database.

Updates on filtering by taxonomy can be seen via the tutorials. Here is one example.

Here is some history on the D_x__ schema.

-Cheers!
-Mike

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3

That makes perfect sense! My peers are using the pre-compiled 138 silva which I believe is no longer recommended. I did follow the tutorial you've mentioned to compile 138.2.

Thank you so much for the clarification!

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