HiC merging bins

[kunaltin2012]

Hi,
Thanks for developing such a nice user friendly tool. I tried running diagnostic plot and then plotted corrected matrix at 10Mb scale. In the diagnostic plot I see total counts per bin at around 40 at 40kb resolution. When I increase the resolution to 100kb the average total counts per bin becomes 20. However, in your tutorial it was around 500. But when I plot matrix I don't see much of interactions in the diagonals. Is there some issue with total counts per bin in my sample? I have 5 replicates of each sample with total depth 330mio per sample but i have not merged the replicates yet.

Please suggest me, what should I do to improve the plots ?
Thank you in advance