issue with chimera and primer design

[ahorvath]

Dear @nservant,

I'd like to design PCR primers to test highly enriched chimeras in the HiC libraries.

In my understanding, the easiest way to infer these to look for fragment combinations in the allvalid files. If I pick such a chimera and check the listed reads, the read pair is often aligned on one fragment, instead of one is on fragment #1 and the other is on fragment #2 HIC_primers.docx)

Shouldn't these be classified as Dangling Ends?

Many thanks for your time and for the great pipeline.

Best,
Attila