Sequence trimming and mapping
Paired-end reads were trimmed for quality, and adapter sequences were removed with a minimum quality base of Q = 20 and a minimum read length of 50 bp using the software Trimmomatic (Bolger et al., 2014). Trimmed reads were then mapped to the D. mojavensis reference genome (Allan and Matzkin, 2019) (SRP190536) using the splice-aware mapperGSNAP (Wu and Nacu, 2010) with the option of new splice events detection. Generated sam files were converted to bam format after indexing and filtering for a minimum mapping quality of MQ = 20 using SAMtools (Li et al., 2009). These mapping results were then used for all differential expression and alternative splicing downstream pipelines.