Transforming kraken outputs to krona

Question

[sagi.polani]

Hi all,

I'm trying to generate a krona plot with multiple sample data generated by kraken.

For this, I understand that I need to use the ktImportText command by krona, but it doesn't seem to work as smoothyl as with the ktImportTaxonomy command.

With ktImportTaxonomy I normally do:

ktImportTaxonomy -q 2 -t 3 results.kraken -o output.plot.html

This works just fine.

But with ktImportText:

ktImportText results.kraken -o output.plot.html

I get an empty plot... :(

Does anyone know if I need to reformat the results.kraken files for this or anything else in that matter?

Thanks!

Sagi

Answer 1

[Vasisht]

ktImportTaxonomy can also be used for creating a krona plot from multiple samples. ktImportTaxonomy -q 2 -t 3 Sample1.txt Sample2.txt -o krona.html

ktImportText relies on a different format than the kraken results files.