Hi all, I have paired-end reads of chromosome 3 in human, and want to extract the deletion, insertion, inversion and translocation in it. For finding if the insertion is happened, I want to extract the paired reads that one pair aligned to chromosome and the other one doesn't. I chose hisat2 for alignment and used --un and --un-conc options, but none of them helped me, because the path regarding to --un is empty, and all the reads in the path of --un-conc are paired (but I need to know which pair is aligned and which one is not). Could you please help me to find a better way to find insertion or to find only one pair of paired end reads which is aligned to chromosome? Thanks