The transcriptional and translational landscape of equine torovirus

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

Transcription junctions were defined as "donor/acceptor" pairs that were either 645 supported by at least 10 chimaeric reads or contained the entire 5' leader and TRS 646 sequence in the 5' segment of the read. At some positions single nucleotide 647 resolution for the chimaeric break-point could not be established; where reads were 648 found to break at adjacent possible positions these positions were merged to give a 649 short region containing the breakpoint. The number of non-chimaeric reads spanning 650 each donor and acceptor site was calculated as the number of reads which 651 overlapped the site by at least 12 nt in either direction (as chimaeric reads 652 overlapping the site by < 12 nt are not detectable). The proportion of chimaeric 653 reads at each "donor" or "acceptor" site is therefore the number of chimaeric reads 654 with a breakpoint at the site divided by this number plus the number of non-655 chimaeric reads spanning the site ( Figure 4B ). 656