I am unfamiliar with BAM files and pretty new to the linux command line. I have what I suspect is a fairly simple problem to solve. I have a dataset where I believe there are a large number of reads mapping to multiple genes. I am trying to find a way to filter for reads that map to more than one gene. Thanks for any help!
Edit: This is data from a scRNA sequencing experiment done with 10X equipment. The cells were from a rabbit which is not supported by 10X for genome alignment so I made a custom reference genome. I had a low rate of mapping to the genome (~20%) and I am trying to figure out the cause - if it is an issue with the reference or our sample. I think there is a possibility that the multiple mapping is due to overlapping annotations in the reference genome (this was suggested to me by 10X support) in which case I don't want to be filtering out those reads I want to fix the reference. But here I am trying to identify if that is actually the case and if so if there are a particular set of genes that are the problem.