RNA-Seq Data Processing Pipeline

Raw reads quality was visually inspected by means of FastQC software⁶⁸ and then processed to remove low quality bases and contaminants (Illumina adapters). Cleaning phase was then performed with Trimmomatic software version 0.36^{69 (link)} using an average quality cut-off of 30 (Phred score) and a minimum read length of 40 bp. Cleaned reads were then mapped against predicted mRNAs (PN40024 12X v2 grape reference transcriptome) obtained from the gene prediction version 2.0 of the National Centre for Biotechnology Information. Mapping was performed using Bowtie2^{70 (link)} tool with default parameters. Alignments were first converted in a binary alignment map (BAM), a binary representation of the Sequence Alignment/MAP (SAM), and then sorted and indexed for the count of reads per mRNA, using SAMtools^{71 (link)} software package. The number of reads aligning to each transcript were counted using an ad hoc Python script.