The transcriptional and translational landscape of equine torovirus

Hazel Stewart; Katherine Brown; Adam M. Dinan; Nerea Irigoyen; Eric J. Snijder; Andrew E. Firth

Ribo-seq density and RNA-seq density were calculated for each gene in the EToV 586 genome (Figure 3, Figure 8) . To normalise for different library sizes, reads per million 587 mapped reads (RPM) values were calculated using the sum of positive-sense virus 588 RNA reads and host RefSeq mRNA reads as the denominator. In order to standardise 589 the regions used to calculate RNA-seq and Ribo-seq density, the following regions were calculated as the number of reads per million mapped reads for which the 5' 605 end maps to each region, divided by the length of the region in nt, multiplied by 606 1000 (i.e. RPKM). For RNA-seq, a decumulation strategy was used to subtract the 607 estimated RNA-seq density for longer overlapping genomic and subgenomic 608 transcripts that would contribute to the RNA-seq density measured for each of the 3' 609