Read Counts from BAM file

Question

[Smriti]

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...?

[ATpoint]

Please do this: How to count fastq reads and then report back to see whether here is really a problem with the sequencing data or just an alignment issue.

Do it on all fastq files from that run, then sum up.