Gene expression in cornea of BALB/c and C57BL/6N mice

Gene expression was quanitified in 4 naive corneas from BALB/c and 4 corneas from C57BL/6N mice without intervention by RNAseq of total RNA with the Ovation Kit for model organisms. To avoid false positive differential expression from better alignment of the reads from C57BL/6 mice to the reference representing a closely related strain while retaining the applicability of the standard reference genome annotation, two pseudogenomes were generated incorporating the known variants into the reference and aligning to the resulting genomes. BAM files were then converted with Lapels to the standard reference, which includes conversion of genome coordinates and adjusting CIGAR strings. Then expression quantification is possible with respect to the standard gene model (here Ensembl version 94) again. Gene expression by sequencing of total RNA fron cornea in two classical inbred mouse strains.