I successfully ran hichipper on validpairs file from HIC-Pro. At the end I got "filt.intra.loop_counts.bedpe". As per my understanding this file contains filtered, significant interactions. I would like to know if there will be a p-value or some sort of stat ? I saw that mango gives a adj.p-values for interactions.
If I want to get more stringent interactions, what would be the best way to filter this file further ? I see some noise in the output and I want to get more stringent interactions.
I successfully ran hichipper on validpairs file from HIC-Pro. At the end I got "filt.intra.loop_counts.bedpe". As per my understanding this file contains filtered, significant interactions. I would like to know if there will be a p-value or some sort of stat ? I saw that mango gives a adj.p-values for interactions.
If I want to get more stringent interactions, what would be the best way to filter this file further ? I see some noise in the output and I want to get more stringent interactions.
Thanks,