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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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Count dismatch between single kaiju and kaiju-multi #185

Open jjuhh opened 3 years ago

jjuhh commented 3 years ago

Hi, Kaiju team.

Using a "kaiju-multi" has the same number of lines(reads) in output file as using single "kaiju"

wc -l sample.A.kaiju.out
> 1635254
wc -l sample.B.kaiju.out
> 1949596
wc -l sample.A.B.kaiju.out
> 3584850

but, the values of counts(column 3) and percentage(coulmn 2) was not same. (after kaiju2table)

fgrep -w "67082" sample.A.kaiju.out.table
> sample.A.kaiju.out.table  0.342276    6673    67082   NA;BeAn 58058 virus
fgrep -w "67082" sample.B.kaiju.out.table
>sample.B.kaiju.out.table  0.802077 13116   67082   NA;BeAn 58058 virus
fgrep -w "67082" sample.A.B.kaiju.out.table
> sample.A.B.kaiju.out.table  0.740505  26546   67082   BeAn 58058 virus

Why is this results? and if both results are not wrong, which one is better to use, kaiju or kaiju-multi, when comparing the virome of case control study?

pmenzel commented 3 years ago

Hi,

would it be possible to send me the zipped output files of kaiju and kaiju2table?