60 (Supplemental Table 1). Many users would accept these lower values unless they filtered by MAPQ after running HISAT2 with default parameters. More concerning was the observation that summary counts for several individual genes had a substantial misassignment due to human reads matching mouse genome (Supplemental Table 2). The top five genes on this list (Table 2) exhibited a surprisingly high proportion of misaligned reads, ranging from ~8% to over 65%. Clearly, using a mixed reference genome allows for cross-alignment of reads to the wrong species, and for some genes this can produce a substantial source of error.
