not primary alignment flag filtering does not work
I have a bowtie2 result looking like this;
27823422 reads; of these: 27823422 (100.00%) were unpaired; of these: 2464773 (8.86%) aligned 0 times 19083986 (68.59%) aligned exactly 1 time 6274663 (22.55%) aligned >1 times 91.14% overall alignment rate
I am trying to count the uniquely mapped reads, and in this case I think the value should be 19083986 since it should be aligned once.
I have tried these commands;
samtools view -h -F 256 -c input.bam samtools view -h -F 0x100 -c input.bam
But they are both giving the total (27823422) number. Why could it be like that?
Thank you in advance.
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