FIG 6.

Improper quantification of fragments that span multiple features. (A) Using the wBm stranded RNA-Seq data set, the log₂ read depth (orange) was plotted across the wBm gene Wbm7023 and its adjacent genes Wbm0608 and Wbm0609. (B) The counts for the three genes as determined by each of the quantification methods were calculated. The counts assigned to Wbm7023 are all derived from fragments that also map to the 3′ end of Wbm0608. Despite the wBm annotation lacking UTRs, these reads likely originate from the 3′ UTR of Wbm0608, indicating that most if not all the reads assigned to Wbm7023 are erroneous.