I have a kraken 2 output (k2report.txt file that looks like this:
What I want to do is to extract only number of reads for example for Genus i.e. G with taxid 2316020, 2719313, 207244 and 572511 and so on. I am not interested in D, O or R etc.
I have a large file with many hundred Genuses. Does anyone has any shell/python script that I could use to extract only Genus abundance (number of reads) for sample1, sample2 and sample3?
I would really appreciate your help.