Total number of duplicates in ChIPQC differs from multiqc ? I check all chromosomes not just one...

In fact 0 duplicates are found with ChIPQC ? How ChiPQC retrieve duplicate ? How can it be explain ? 

Also RelCC is Inf for one of my sample , what does it mean ?

Hi,

Chipqc looks for SAM flags marking reads as duplicates as provided by Picard's markdupicates tool.

So it will report only if reads have been marked so then I suspect  duplicated rate is zero because of this here

We will move to  some of the code  for duplicate counting without marking in the very near future

A negative score often suggests a low enrichment, could you share the figure with me privately and I can take a look?

Best 

Tom