Fig. 3.

Comparison of the ISoLDE and Bonthuis methods using the Bonthuis DRN dataset. (A) Output of the resampling version of ISoLDE on the Bonthuis dataset. For each gene, the variability (denominator value of SG statistics) is plotted against the allelic bias (numerator value of the S_g statistics). Violet crosses correspond to bi-allelically expressed genes (BA). Red and blue crosses correspond to genes called maternally and paternally biased (AI), respectively. Gray crosses label undetermined genes (UN). Gray circled crosses correspond to flagged genes (consistency or significance flag). (B) Discordant ISoLDE and Bonthuis calls. The Bonthuis dataset was analyzed using the re-sampling version of ISoLDE. Genes that were called AI by only one of the two methods are indicated by colored circles on the ISoLDE output. See the figure for color code (first call is ISoLDE call). Numbers in brackets are the number of genes in each category. (C) The fractions of maternal and paternal reads in each replicate sample of the Bonthuis dataset are displayed in red and blue, respectively. The black dashed line corresponds to an unbiased parental origin, i.e. a bi-allelic expression. A gene from each type of discordance in this dataset has been chosen. F1r and F1i in the replicate names refer to the reciprocal crosses