Question: Kraken output to Krona Tools: What can be selected as magnitude
1
gravatar for deepthithomaskannan
4.0 years ago by
Canada
deepthithomaskannan250 wrote:

Hi all,

I am trying to use Kraken (http://ccb.jhu.edu/software/kraken/) output file as an input to KronaTools (metagenomic visualization tool)script ktImportTaxonomy.  Basically I am doing the taxonomy classification using Kraken and trying to visualize it using Krona tools.  I would like to know what kind of values I can use as magnitudes for the ktImportTaxonomy script in KronaTools.

Kraken output formatt is:

Each sequence classified by Kraken results in a single line of
output.  Output lines contain five tab-delimited fields; from
left to right, they are:

  1) "C"/"U": one letter code indicating that the sequence was
     either classified or unclassified.
  2) The sequence ID, obtained from the FASTA/FASTQ header.
  3) The taxonomy ID Kraken used to label the sequence; this is
     0 if the sequence is unclassified.
  4) The length of the sequence in bp.
  5) A space-delimited list indicating the LCA mapping of each k-mer
     in the sequence.  For example, "562:13 561:4 A:31 0:1 562:3"
     would indicate that:
     - the first 13 k-mers mapped to taxonomy ID #562
     - the next 4 k-mers mapped to taxonomy ID #561
     - the next 31 k-mers contained an ambiguous nucleotide
     - the next k-mer was not in the database
     - the last 3 k-mers mapped to taxonomy ID #562


I selected fields 2 and 3 as input to KronaTools. My command is:

ktImportTaxonomy <file_contain_field2&3FromKraken> -o Output_taxonomy.krona.html. 

In Krona tools there is an option for giving magnitudes.  Can I select any of the fields as magnitude from the Kraken output?

Thanks,

Deepthi

kraken magnitude krona • 3.1k views
ADD COMMENTlink written 4.0 years ago by deepthithomaskannan250
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