Krona charts with qiime2


(Lotte Geerlings) #1

Hello everyone!

Thanks to this forum I am nearly done with my pipeline for taxonomic analysis, but I’d like to add Krona and Megan to it as well.

I have 16s data that I managed to turn into the table.qza and taxonomy.qza thanks to the ‘Moving Pictures’ tutorial and I was wondering if someone had a way of turning this into a Krona plot.

I tried following this tutorial:

To export my table to an OTU type table

In combination with https://github.com/GenomicaMicrob/OTUsamples2krona
this script for Krona, but when I open the Krona link, it’s empty…

When I look in my table, it looks like this:

Constructed from biom file

#OTU ID 4 1 2 5 3
d7df3d3c995c5309bf6c00c463e590ff 1891.0 0.0 0.0 0.0 0.0
56afa7b0ec6fd6916b688ee5b1dc4d86 1772.0 0.0 0.0 0.0 0.0
7e61215102597238415a1dcdc4b77d4d 1555.0 0.0 0.0 0.0 0.0
796f8337a482d135bb1035cdd9495dd0 1069.0 0.0 0.0 0.0 0.0
66570f449912d1714dbb23391f78f859 614.0 0.0 0.0 0.0 3.0
cca65ed41b20e76d8a92402857422098 600.0 0.0 0.0 0.0 0.0
4124703303b637444c4ef6a27826b05b 401.0 0.0 0.0 0.0 0.0
0fc6cd199f25a293ae73303250f616e9 292.0 0.0 0.0 3.0 0.0
d6f9e69dc1acd1f29c62fe6ba1a011dc 280.0 0.0 0.0 0.0 0.0
1c5fbbd938b3889551b48c4ff102647f 213.0 0.0 0.0 0.0 0.0
6e078eca2fc0cd8a70b4928cfbfe4108 207.0 0.0 0.0 0.0 0.0

While the table from the tutorial looks like this:

F3D0 F3D9 MOCK domain;phylum;class;order;family;genus;species
2 0 0 Bacteria;Firmicutes;Clostridia;Clostridiales;Clostridiaceae;Unclassified_g;Unclassified_s
0 0 621 Bacteria;Firmicutes;Bacilli;Bacillales;Staphylococcaceae;Unclassified_g;Unclassified_s
0 3 0 Bacteria;Actinobacteria;Coriobacteriia;Coriobacteriales;Coriobacteriaceae;Unclassified_g;Unclassified_s
2 0 0 Bacteria;Bacteroidetes;Bacteroidia;Bacteroidales;S24-7_f;Unclassified_g;Unclassified_s

Can someone (as I assume it went wrong with the making of the table), tell me what needs to be done to create a Krona plot?

Much thanks in advance,

Lotte


(Lotte Geerlings) #2

For those of you wondering, I solved the problem myself (talk about progress!)

It was a problem with the BIOM table, as QIIME1 worked with a json and QIIME2 with a different type of file that wasn’t compatible to KRONA.