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 param
Transcriptome sequencing (RNA-Seq) overcomes limitations of previously used RNA quantification methods and provides one experimental framework for both high-throughput characterization and quantificat