I used the featureCounts function from the Rsubread package in order to count reads. The first time I used my 'regular' bam files. The second time I used Picard Tools to mark duplicates in each bam file and used this data as substrate. I am getting the same number of counts in both cases using featureCounts. I was wondering if it is possible to tell featureCounts to exclude duplicates from the counting. Is there an option doing it within Rsubread or do I have to actually remove (as opposed to mark) the duplicate reads?