Sequencing and Alignment of Drosophila Transcriptome

Per-read per-sample FASTQ files were generated using the Illumina bcl2fastq conversion software (v2.20) to convert per-cycle BCL base-call files outputted by the sequencing instrument into the FASTQ format. The alignment program STAR (v2.4.5a) (Dobin et al. 2013 (link)) was used for mapping reads to the D. melanogaster reference genome dm6 (Dos Santos et al. 2015 (link)) and the application FastQ Screen (v0.5.2) (Wingett and Andrews 2018 (link)) was used to check for contaminants. The software featureCounts (Subread package v1.4.6-p3) (Liao et al. 2013 (link), 2014 (link)) was used to generate the matrix of read counts for annotated genomic features.