Alignment of RNA-Seq Reads to the Rat Genome^a.

aPaired-end reads were aligned to Rn4 using TopHat v1.3.2 and unique, non-gapped alignments were obtained. TopHat parameters were: -g 1–r 200–best –strata, where ‘-best’ and ‘–strata’ are bowtie parameters that were included in the TopHat source code. Each sample represents an individual RNA-Seq lane of liver mRNA from one animal. The last three columns indicate the number of reads in which both ends were mapped; only one end was mapped but not both (singletons); and reads that were spliced to allow for alignment, respectively.