Question: Transforming kraken outputs to krona
0
gravatar for sagi.polani
3.6 years ago by
sagi.polani80
Israel
sagi.polani80 wrote:

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

kraken krona • 5.3k views
ADD COMMENTlink modified 3.0 years ago by Vasisht170 • written 3.6 years ago by sagi.polani80
2
gravatar for Vasisht
3.0 years ago by
Vasisht170
Vasisht170 wrote:

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.

ADD COMMENTlink written 3.0 years ago by Vasisht170
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2242 users visited in the last hour