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?