Fig. 1

Bioinformatic subtraction pipeline to infer Y-linked transcripts. Male RNA-seq reads are mapped to genomic scaffolds build from female genomic reads (Step 1); unmapped male RNA-seq reads are used to build a de novo transcriptome (Step 2), and transcripts that either map to the female genome assembly (Step 3) or female RNA-seq reads (Step 4) are discarded. Remaining transcripts are merged (Step 5) and only merged transcripts are kept that show mapping to male genomic reads and no mapping to female genomic reads (Step 6) and that show expression in males but not females (Step 7). Transcripts that mapped to a de novo repeat library were discarded (Step 8), and only transcripts which had an effective length (as calculated by the software eXpress) greater than 0.6 times the transcript length were kept in the final list (Step 9)