The reads from each replicate experiment were separately aligned to the reference genome mm929 and corresponding transcriptome using the short-read aligners ELAND v2e (Illumina) and Bowtie30. Reads uniquely aligned by both tools to known exons or splice junctions with no more than two mismatches were included in the transcriptome. Reads uniquely aligned but with more than two mismatches, or reads matching several locations in the reference genome, were removed from the analysis. The percentage of reads assigned to the reference genome and transcriptome using this protocol is reported for each group of replicates (Supplemental Fig S6B) with the corresponding percentage of covered genes (Supplemental Fig S6B).
