My group is currently using DropEst to process some single-cell data from erythroid differentiation, so two of our key marker genes are alpha and beta globin. Both genes are present in two identical, duplicate copies, so reads that map to these genes are output twice in our alignment bam, and one of the two alignments is randomly marked as the primary alignment. However, the globin genes are missing from the count matrix files after running dropEst - so I'm guessing multimapped reads are getting discarded? Is there a way to get DropEst to count all the primary alignments (and primary alignments only) regardless of whether the read is uniquely mapped?