What Is The Expected Distribution Of The Distance Between Aligned Paired-End Reads?

Question

[Pfs]

Hello,

I tried to plot the distribution of the distance between mates among mapped reads (RNASEQ) and I noticed many different distributions.

I was expecting the distance being centered at x, where x is the insert size.

Is this true for all chromosomes? How about those reads that map mitochondria DNA?

THANKS!

[Aaronquinlan]

If your experiment worked, would the distances not merely reflect the distances between exons? If so, that would almost certainly be a multi-modal distribution.

[Jeremy Leipzig]

your saying the distances varied between different chromosomes?

[Jeremy Leipzig]

you're saying the distances varied between different chromosomes?

Answer 1

[Chris Miller]

Let's say your insert size is 100 bp starting out. You get your reads from the RNA, then map those reads back to the reference genome. You'll quickly figure out that many of the paired reads have ends mapping to two different exons. This means that if you take the mapping distance between the reads, your distance is going to be 100 bp (your insert size) PLUS the size of the intron between the exons.

The median intron size is about 1300bp, but is highly variable, so you're not going to get a clean peak around your insert size.