We identified exon-introns junctions by mapping annotated transcripts (r3.03; Flybase) and transcripts of Y-linked genes from NCBI (gi|295126506|gb|GU937420.1|, gi|255764727|gb|EU595397.2|, gi|295126512|gb|GU937423.1|) to our assembly using exonerate 2.4.0. To complement these data, we mapped RNA-seq reads to our assembly using Tophat v2.0.13. We annotated transcripts, eliminated small redundant isoforms with cufflinks v2.2.2
