lower mapping rates in salmon v0.13 compared to previous versions
[Most likely answer based on comments attached to the question]
Hi Courtney, We've looked into the data and identified the source of the different mapping rates. Specifically, the cause is discordant reads; in this case reads that are dovetailing with respect to their positions on the reference. If you run Bowtie2 with &quot;RNA-seq&quot; flags (i.e. disallowing discordant mappings), then you get essentially the same mapping rate as salmon here. Is allowing dovetailing reads something that should be very important in your analysis? If so, we can consider what would be necessary to add back support, but generally, they provide evidence of tenuous quality.