There appear to be different numbers of interactions reported in the seqmonk and washU format files (taking into account the 2 line vs 1 line format). Is this the expected outcome or should the numbers of interactions match?
The table below shows the line counts for a selection of my output files. Seqmonk and ibed are the same, but washU is consistently off by a few thousand
washU seqmonk seqmonk/2 ibed data1 123142 254394 127197 127198 data2 137212 281394 140697 140698 data3 149581 305370 152685 152686 dataMerged 171783 356412 178206 178207