for a set of samples, paired end nextseq illumina p2 was performed. in all, i am getting read count much higher than my actual flow cell capacity. How is it even possible?
my flow cell can generate total reads upto one billion (paired-end), and i see a total of 12 billion!
this was the command to get total and primary aligned reads. the exact figure i got from Qualimap as well.
samtools view -c sample1.bam samtools view -c -F 260 sample1.bam
can anyone comment on this...?