Error in Biostrings
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Hi all,
Even in these horrific times of COVID-19 pandemic we try to focus on our research.
The DADA2 pipeline Tutorial was very useful but now I am struggling big time on the phyloseq part.
I just removed all Eukaryota en NA from my data set:
ps_EPSO1_noEuks_noUnk <- subset_taxa(ps_EPSO1, Kingdom!="Eukaryota" &
Phylum!=" ")
print(ps_EPSO1_noEuks_noUnk)
phyloseq-class experiment-level object
otu_table() OTU Table: [ 3455 taxa and 40 samples ]
sample_data() Sample Data: [ 40 samples by 13 sample variables ]
tax_table() Taxonomy Table: [ 3455 taxa by 6 taxonomic ranks ]
refseq() DNAStringSet: [ 3455 reference sequences ]
But I receive on my next step an error:
dna <- Biostrings::DNAStringSet(taxa_names(ps_EPSO1_noEuks_noUnk))
Error in .Call2("new_XStringSet_from_CHARACTER", class(x0), elementType(x0), :
key 51 (char '3') not in lookup table
If I look at my ps_EPSO1_noEuks_noUnk, my pay_tree is NULL. I have no idea how come.
Some help would be much appreciated!
BW
H.
This is not an issue with the Bioconductor website which is what this repo is for. Could you please repost this is the Biostrings github repository. https://github.com/Bioconductor/Biostrings