Fig. 6

Validation of allele-specific transcription level calculations and integration with ChIP-seq and WGBS datasets at allelic resolution. MEA was extended to accommodate contemporary RNA-seq aligners and to automatically organize allelic and total genomic tracks into UCSC Track Hubs to aid data visualization and interpretation. a The number of annotated genic exons covered by allelic reads using BWA, Tophat2 and STAR aligners is shown for an RNA-seq dataset generated from C57BL/6 J x DBA/2 J ICM cells [48]. b UCSC genome browser screenshot of the Meg3 gDMR and downstream gene using the default MEA output for visualization of allelic (WGBS, RNA- and ChIP-seq) data. MEA automatically generates composite tracks containing total (allele-agnostic, grey), reference (blue) and non-reference (red) genomic tracks for visualization of allelic RNA- and ChIP-seq datasets. Bottom three tracks show MEA output from previously published C57BL/6 J x PWK/PhJ F1 ICM ChIP-seq data [13, 47]