Question: Qiime file for Krona pie chart?
1
gravatar for manekineko
4.4 years ago by
manekineko130
manekineko130 wrote:

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 • 4.1k views
ADD COMMENTlink modified 7 months ago by jeremieaauger10 • written 4.4 years ago by manekineko130

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

ADD REPLYlink written 4.4 years ago by Daniel3.8k

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! :)

ADD REPLYlink modified 16 months ago • written 16 months ago by jeremieauger20

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

ADD REPLYlink written 7 months ago by nisrinalulu10
6
gravatar for ferstar
3.2 years ago by
ferstar50
China/Xi'an/NWU
ferstar50 wrote:

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
ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by ferstar50

krona is awesome! I used it with kraken output glad to know qiime output can be used as well

ADD REPLYlink written 3.2 years ago by badribio240

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

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by ferstar50

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

ADD REPLYlink written 2.7 years ago by arunsaikirans0

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

ADD REPLYlink written 2.7 years ago by badribio240

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

ADD REPLYlink written 2.7 years ago by arunsaikirans0
1
gravatar for lakhujanivijay
3.8 years ago by
lakhujanivijay5.2k
India
lakhujanivijay5.2k wrote:

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).

ADD COMMENTlink written 3.8 years ago by lakhujanivijay5.2k

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

ADD REPLYlink written 2.7 years ago by arunsaikirans0
0
gravatar for jeremieaauger
7 months ago by
Canada, Montréal
jeremieaauger10 wrote:

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

ADD COMMENTlink written 7 months ago by jeremieaauger10
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