Hi~ I'm currently using 10x cellranger to analyse single cell RNA-seq data. According to their algorithm, reads mapping confidently to more than one exons will be discarded. However, there are paralogous genes in the genome that are largely identical and all the reads for such genes are discarded. Therefore, I was wondering if there is a way to change the algorithm to count the first (or a random) confident alignment. Unfortunately, I wasn't able to locate the file containing the algorithm. Any hints would be appreciated. Thanks every one!
The cellranger UMI deduplication algorithm does not handle reads that map among multiple genes, there is no "easy" way to handle this situation. You may be interested in taking a look at our quantification tool, alevin, which we've designed, in part, to help deal with these cases. In addition to having a methodology for handling reads that map between multiple genes, it is much faster than cellranger.
I don't think cellranger can do this - but the tool Alevin (github, biorxive paper) does support multi-mapping read/UMIs since it builds on Salmon quantification. Since it builds on Salmon the quantifications will also be more accurate (and much faster).