I am running fitHiChIP on publicly available datasets found at https://hichip.readthedocs.io/en/latest/data_sets.html I have gotten CTCF to work well and produce arcs but when running fitHiChIP for H3K4me3 and H3K27ac I have used the following settings and have found almost no arcs. I know from previous reports that there should be many peaks in the region I am looking in but the results I am getting are showing less than 20 peaks for all of chromosome 9. If you could give me some pointers as to what I may be doing wrong? My pairs file is a HiCPro-like file made by the tutorial linked above

my ChIP peak file is the appropriate file from the link above

IntType=5 but I am analyzing the Peak to all and all to all

BINSIZE=5000

LowDistThr=10000 (I have also tried 20kb)

UppDistThr=3000000 (I have also tried 2Mb)

UseP2PBackgrnd=0

BiasType=1

MergeInt=1

QVALUE=0.01

Thank you in advance for your help. I tried these parameters for both H3K27ac and H3K4me3 and both results in very very few peaks. I apologize if this is an obvious answer