Abstract
Bases are called using Illumina pipeline Casava 1.8.Reads are mapped to the drosophila genome using Tophat2. Refseq annotations of known exon junctions are provided with -G option.Number of reads on each gene were counted using custom script, and differentially expressed genes were called using edgeR.Genome_build: Dm3Supplementary_files_format_and_content: tab-delimited text file listing the number of reads on each gene