Hichipper with HiCUP input

[rdali]

Hello Caleb,

We are interested in running hichipper on our HiChIP data. However, your pipelines (Hi-C, capture HiC and HiChIP) are based on HiCUP which results in a bam that contains all the Valid reads. Is it possible to use hichipper with HiCUP? If you can think of a quick fix then I can help edit the code for our internal version to include hichipper in our institute's workflow.

Thanks! Rola