read mapping - What is the correct way to map Hi-C data with bwa mem?

Library PrepI have a Hi-C library prepped using an enzyme that cuts at GATC, so it leaves GATCGATC as the junction sequences. This library was sequenced on a 2x150 PE Illumina run.Data Pre-processingThe reads were adapter and quality trimming with trimmomatic paired-end mode, keeping reads that overlap. Finally, the forward and reverse reads were trimmed such that all bases 3' of the junction sequence (GATCGATC). For example, the read:5' AAAATT**GATCGATC**AATTATGGATAA 3' becomes: 5' AAAATT**GATC 3'In this process, sequences that don't contain t...Read more