Hello, I'm doing mapping & Calling of my data, but, I have some question about my data.
Here is the result of "samtools flagstats" of my bam file (created by bwa aln)
but, I fount that two files have different read counts. although it is paired-end data.
I believed that paired-end sequencing data must have same amount of reads, but, my data does not. And, as you can see that there is a lot of singletons and very small proportion of "properly paired"
Does my data have problem? Should I remove my data and try again..?
Only 2.9% are properly paired. This is bad. You could tell use a bit more about your sequencing project and application and especially ref used so we can help.