Command jobs used to generate differential expression data in experiment 1.

For experiment 1, we used only the OGS 2.0 annotation, and varied only whether the data from replicate 1 was included (present in Analysis 1, absent in Analysis 2). At this time cufflinks2 was used to assemble and quantify transcripts. Due to sub-optimality of the raw data, we did not do as many variations on the analysis as were done for Experiment 2.