I do have a question on finding significant HiC interactions using HOMER tools.
When I use HOMER tool's "analyzeHiC" program to capture significant HiC interactions at P <= 0.001 cutoff, in the output file at the column # 19 it provide FDR (calculated by Benjamini method with no. of analysed tests i.e., 400 million tests) values for all the significant interactions.
The FDR value is always between 0 and 1 and maximum (~90%) of the HiC interactions are with the FDR value "1". Does it mean that all these interactions are significant but with false discovery rate 100%??
Should I consider HiC interactions, found with P <= 0.001, significant ?? OR Should I also consider these strange value of FDR ??
Thanks in advance for helping me.