Fig. 2

Validation of epiTEome on simulated data. a Bar plot of sensitivity of detection for simulated TE insertions at three different TE insertion contexts (gene, intergenic, TE). SPLITREADER and TEPID use non-bisulfite converted reads, while epiTEome utilizes bisulfite-converted MethylC-seq reads. b FDR of epiTEome, SPLITREADER, and TEPID calculated from the same simulated data as part A. Error bars in (a) and (b) represent the 95% confidence interval (CI) generated using five replicates. c Analysis of how the variables of sequencing depth, read length, methylation level, and number of SNPs affect epiTEome sensitivity. Throughout the analysis in (c), epiTEome produced a 2.88% false-positive average, with a standard deviation of 1.45