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!