Additional file 5: Figure S5. of Tools and best practices for data processing in allelic expression analysis

Comparison of AE data generated with different alignment strategies. a–d For each comparison the observed reference ratios for het-SNPs that have AE data in both strategies are plotted against each other (Shared het-SNPs), histograms show the reference ratios of sites that are unique to only one analysis (Unique het-SNPs), and a density plot shows the genome wide reference ratio distribution for each analysis. AS = personalized genome generated with Allele-Seq and phased genotype data, GSNAP vAWARE = GSNAP using variant aware alignment. No filtering of sites has been done. All data come from Geuvadis LCL RNA-seq libraries from NA06986. Only het-SNPs with eight or more reads are included. (TIFF 15560 kb