I have a relatively small capture HiC library (DpnII digest) covering almost 3000 DpnII fragments or about 1 Mb. From 155 M reads using minfraglength 40, maxfraglength 930 and default bin size, Chicago calls 36K interactions. This value seems higher than expected. I’ve tested downsampling my raw reads and find that the number of interactions never reaches a plateau as I increase raw reads. Could you give me some advice on whether anyone has used Chicago for relatively small capture libraries and whether the small capture region affects the background model?