I am interested to calculate inner mate distance for paired-end reads in many bam files i.e. distance from the right-most end of the left read to the left-most end of the right read and all the properly paired QC-passed reads that map in the bam file (ref: Calculating inner mate distance for paired reads)
I have used CollectInsertSizeMetrics.jar (ref: Picard MarkDuplicates error after using bamaddrg: "bin field of BAM record does not equal value computed..." ) and got the attached insert size histogram for one of my bam files (which includes properly-paired QC-passed reads, sorted and indexed). However, I am unable to understand the histogram properly.
In this post: Mystery: What is going on with this Insert Size Metrics Histogram, I can see both FR and RF in the histogram, but not in mine.
Please guide for the possible explanations.