So I'm currently analyzing some ATAC-seq data. The duplicated reads were removed using first samtools fixmate -m and then samtools markdup -rs. I'm facing many discarded reads and I cannot repeat this step anymore, maybe in the future. I was wondering, are there any known differences between this methods and other such as PICARD's MarkDuplicates?
Would be worth trying other methods for removing duplicated reads, or the % should be the same?
Any advice would be appreciated.