problem opening taxonomy file from Silva
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Hi @jbisanz
qza_to_phyloseq and read_qza do not manage to open correctly my silva taxonomy file. I got a warning message (see attached). It creates the phyloseq object but the taxonomy has 8335 rows (= ASVs) instead of 34550. I converted my qza file to tsv file and checked that it contains effectively 34550 ASVs.
I think it is because there is a unusual character in row 8335. Basically the taxonomy is "D_6__[Clostridium] piliforme (Tyzzer's bacillus)". I wonder if it is because the functions can not handle the ' ?
Could you advise on what I can do? I am happy to send you my qza file but I do not manage with this platform.
Many thanks for your help.
A.
Hi Alice, that is very odd, could you send me the artifact and I'll see what I can do?
Jordan
All fixed!