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bioinformatics-centre / kaiju

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
http://kaiju.binf.ku.dk
GNU General Public License v3.0
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abundances #54

Closed ghost closed 6 years ago

ghost commented 6 years ago

hi

is there a way to convert the %mapped reads output to abundances?

pmenzel commented 6 years ago

Uhm, did you try the kaijuReport tool or use Kronatools?

ghost commented 6 years ago

Hi yes I did use the kaijuReport tool. It prints out the number and percent of reads mapped. Are we assuming %reads is the same as relative abundance?

Thank you.

On Nov 27, 2017 04:19, "Peter Menzel" notifications@github.com wrote:

Uhm, did you try the kaijuReport tool or use Kronatools?

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pmenzel commented 6 years ago

Yes, the percentage of classified reads for a taxon would be the equivalent of relative taxon abundance in this kind of analysis.

ghost commented 6 years ago

Thank you Peter.

On Mon, Nov 27, 2017 at 9:10 AM, Peter Menzel notifications@github.com wrote:

Yes, the percentage of classified reads for a taxon would be the equivalent of relative taxon abundance in this kind of analysis.

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