Qiime file for Krona pie chart?
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6.5 years ago
manekineko ▴ 150

Hi,

I have analysis with Qiime of 16s reads, and I want to make a pie chart with Krona but do not know which file from Qiime to use for Krona?

qiime krona • 6.7k views
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You'll be more successful asking at the qiime forum: https://groups.google.com/forum/#!forum/qiime-forum

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Are you still trying to get it working? I know I had to make it work and figureD out how! Anyways without having to write / debug bash script! There is an R package that does Krona charts! Let me know if you wan tot know more! I'll report on my method if needed! :)

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Dear Jeremieauger,

I also working using Krona but with MEGAN output. I face some problem because my command didn't work in Krona. I wonder what the R package that does Krona chart that you told?

Thank you,

Regards,

Lulu

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5.4 years ago
ferstar ▴ 60

Hi, hope this answer is not too late. :)

convert biom to tsv format

biom convert -i single_sample.biom -o single_sample.tsv --to-tsv --table-type "OTU table" --header-key taxonomy

remove the first two rows with comment

# take a look at single_sample.tsv
$ head single_sample.tsv 
# Constructed from biom file
#OTU ID H2O taxonomy
346085  140.0   Bacteria; Proteobacteria; Alphaproteobacteria; Caulobacterales; Caulobacteraceae; Brevundimonas; Brevundimonas_bullata
10298   2.0 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Photorhabdus; Photorhabdus_temperata
122823  3.0 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Oxalobacteraceae; Massilia; EF516371_s
130468  2.0 Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Sphingopyxis; Sphingopyxis_witflariensis
139977  38.0    Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales; Erythrobacteraceae; Erythrobacter; Erythrobacter_flavus
121751  2.0 Bacteria; Firmicutes; Clostridia; Clostridiales; Lachnospiraceae; Catonella; JX096343_s
96934   10.0    Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas; Pseudomonas_guguanensis
95181   4.0 Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Moraxellaceae; Acinetobacter; Acinetobacter_radioresistens

# remove the comments
$ egrep -v "^#" single_sample.tsv > sample_no_comment.tsv

remove the first column

$ cut sample_no_comment.tsv -f 2- > sample.tsv
$ head -n2 sample.tsv 
140.0   Bacteria; Proteobacteria; Alphaproteobacteria; Caulobacterales; Caulobacteraceae; Brevundimonas; Brevundimonas_bullata
2.0 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Photorhabdus; Photorhabdus_temperata

replace the "; " with "\t"

$ sed -i 's/;\s*/\t/g' sample.tsv
$ head -n2 sample.tsv 
140.0   Bacteria    Proteobacteria  Alphaproteobacteria Caulobacterales Caulobacteraceae    Brevundimonas   Brevundimonas_bullata
2.0 Bacteria    Proteobacteria  Gammaproteobacteria Enterobacteriales      Enterobacteriaceae   Photorhabdus    Photorhabdus_temperata

now we can make a pie chart with ktImportText(One of the Krona tools)

$ ktImportText -n enjoy_your_life -o sample.krona.html sample.tsv

open sample.krona.html with your web browser, you'll see this

Krona_snapshot_enjoy_your_life

all in one command(optional)

$ awk -F '\t|;' 'BEGIN{OFS="\t"} FNR > 2 {$1=""; print $0}' single_sample.tsv | cut -f 2- > sample.tsv
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krona is awesome! I used it with kraken output glad to know qiime output can be used as well

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Yeah, its really awesome and I'm glad my solution is useful to you:)

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Hello badribio, Could you please explain how to create kraken output,what is the command to be used??

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What have you done so far, and which step are you stuck?

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I have finished qiime analysis,but I want to know what output file generated by qiime to provide as an input in kraken.

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5.9 years ago

otu_table_L6.txt file generated by the script summarize_taxa.py will be the best file to be used for generating Krona pie chart for obvious reason (having information for all the taxonomic ranks right from phylum to genus).

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Hi Vijay, I have installed Krona and Kraken what is the input file for kraken and krona??

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2.8 years ago

You just have to import your qiime artefacts (table.qza, rooted-tree.qza, taxonomy.qza and sample-metadata.tsv) in the form of a Phyloseq. Then there is a neat package that generates Krona charts:

https://rdrr.io/github/cpauvert/psadd/man/plot_krona.html

I can further develop, but this post seems outdated!

Cheers, -JA

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