In addition, Cufflinks version 2.1.1 was applied to the BAM files to estimate both gene- and isoform-level FPKM values for all Ensembl genes and isoforms. Separately, Cufflinks was applied to the BAM files to assemble isoforms for each sample. These assembled isoforms were unified across samples using Cuffmerge, resulting in a single GTF file of “merged” genes and isoforms annotated by Ensembl annotations. Cufflinks was then applied to this GTF file to estimate both gene- and isoform-level FPKM values for all merged genes and isoforms.
