I have two Paired-end ChIP-seq dataset. One set of data is 2
*36 bp and the other set is 2
*100 bp. I want to compare these data to find deferentially regions, ... but I have this concern that different length might affect downstream analysis.
Should I trim the 100 one to 36? or as far as both of them are PE, it does not matter that much. Would you please share your ideas with me? Thanks