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smdabdoub / kraken-biom

Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
MIT License
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It seems that unclassified reads are ignored #24

Open claczny opened 1 year ago

claczny commented 1 year ago

Thanks a lot for this very handy tool! It makes it very convenient to create a biom file and to then use this in R, especially in combination with the phyloseq and ampvis packages.

I observed an unexpected behavior in that the biom file seems to ignore the Unclassified reads information from the Kraken2 report.

Is this intended or am I missing something?

Thank you very much again!

Best wishes and stay safe,

Cedric

smdabdoub commented 1 year ago

Hi Cedric,

Since kraken-biom is written to collate reads assigned at various taxonomic levels, it does ignore reads that are marked as Unclassified in the kraken reports.

Technically it shouldn't be difficult to include those, I've just never had a use case for them. I suppose I could add a flag like --include_unclassifieds or something.

Shareef