Fig. 12

Computational pipeline for identification of candidate testis-specifically spliced genes. RNA-seq reads were mapped to the relevant reference genome using TopHat. Transcript assemblies were generated using Cufflinks. Transcript expression was quantified using Cuffdiff. The output of these steps, along with user-defined threshold FPKM values, was used as input for a custom Python program. Custom Python scripts in combination with bedtools were used to output a list of candidates with associated information used for further filtering, such as exon-exon junction coverage and expression values, as well as sequences in a convenient format for primer design – intron flanking sequences, and alignments of all splice forms for each gene