Can someone tell me how aligners, such as Bowtie, work on duplicated genes? Let’s say that there are two identical copies of a genes, A and B.
Does Bowtie assign reads that map to this gene randomly to A and B?
Is the mapping quality reduced for reads that map to duplicated genes?
Basically, I am trying to obtain reads to duplicated elements such as ribosomal RNA genes and I would appreciate advise on the best ways to analyze such genes.