Does this output indicate my bam is paired end?

Question

[curious]

I have bams from the same sequence batch, trying to find out if they are paired read

as per this post

samtools view -c -f 1 in.bam

output 53178051 plugged in to this decoder, which seems to say paired read because it contains 1

Oddly, the very next sample produces 47757395

I have several hundred bam from the same batch, about half of then output the 1

Wouldn't this be unexpected if they are all from the same batch?

Answer 1

[swbarnes2]

I don't know if you quite understand what that command line is doing.

Whatever the output of that command is, that is how many paired end reads are in your bam.

[curious]

-> my embarrassment (－‸ლ)