Hello everyone I am analyzing Chip-seq data. In fragmentation step we used Micrococcal Nuclease in this condition can I remove duplicate reads from bam file after mapping or not can anyone suggest me. Read many related papers some people are removing duplicates and some are not confused what to do. PCR showing bands 150, 300, 450, 600 etc. is this fragmentation size matters in chip-seq because more than 1k bands are visible as its almost cutting around random nuleosome position. I need some expert opinion.