HCT15-TKO, OXA 3-1
Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocal from Chepelev et al., Nucleic Acids Research,2055. In short, exons from all isoforms.