Using bowtie and a number of scripts, I have determined the position of donor and acceptor sites in a virus genome and the number of reads that span these sites. I have read through the documentation for MISO and how to use it to produce sashimi plots however in my particular case, I do not want to re-process the BAM file, generate a gff file etc... I would like to produce from the data I have on the donor and acceptor sites, the input for IGV that will enable me to draw a sashimi plot.
I think it is possible to do this using a BED file but I am obviously putting information in the wrong fields as I am not able to get the arcs linking up different sites using the sashimi plot options.
UPDATE: It is not possible to create a sashimi plot from just a bed file. The SAM/BAM file is needed.