Supplementary Information 1
Commands used for the bioinformatics pipeline

#Sample Alignment 
bowtie2 -x MSU7.all.cdna -p 16 -1 rep1.R1.fq.gz  -2 rep1.R2.fq.gz  --no-discordant | samtools view -bS -o output.bam - &
#remove multi-mapped reads (modest approach)
samtools view -b -q 1 -@ 16 ${i}.bam  -o  ${i}.mapq.bam
#Read count quantification using Salmon
salmon quant --libType U --alignments ${i}.mapq.bam --targets MSU7.all.cdna.fa -p 12 --biasCorrect --useErrorModel --output ${i}.salmon
