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marbl / Krona

Interactively explore metagenomes and more from a web browser.
https://github.com/marbl/Krona/wiki
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Krona chart using diamond blast #53

Open spatroca opened 7 years ago

spatroca commented 7 years ago

Hello all,

I am try make Krona chart using blast form diamond. I used the command to DAA output, however, I didn't got convert this file to running in the Krona. Anybody can help me?

Thanks!

WardDeb commented 7 years ago

Hi, We use krona for the exact same purpose. You can convert the DAA to regular blast output using the diamond view option. This converted output can be used directly with krona.

spatroca commented 7 years ago

Thanks, I got convert DAA file using diamond view option. However, I use: ktImportTaxonomy file.input -o file.out.html to plot Krona chart, but showed chart Krona with 100% no hits. I need set any other parameter in this command?

ashishdamania commented 7 years ago

Not sure if this will work: tryktImportBLAST

Also, I wonder if you used --salltitles option when running Diamond.

spatroca commented 7 years ago

I used diamond blastx -d viral.protein.dmnd -q contig.fa -o file -f 100 --salltitles -k 1 after used diamond view -a file.daa -o file_2 returned several row like contig-100_1345 ref|NP_955119.1| 98.4 62 1 0 18 203 1 62 2.4e-28 124.0 I try use ktImportBLAST, but doesn’t work.

ashishdamania commented 7 years ago

Did you try running updateTaxonomy.sh

Is it installed with all helper files? https://github.com/marbl/Krona/wiki/Installing

spatroca commented 7 years ago

Yes, and create taxonomy.tab.

And when I try use ktImportTaxonomy I found in the path.