How to prepare a BED file to make a sashimi plot in IGV?

Question

[Joseph Hughes]

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.

Answer 1

[Juan Felipe Ortiz]

Just for reference. It IS possible. Your bed file has to have a header line

track name=junctions

Then, you go to View - Preferences - Alignments, and allow show junctions track. Then, right-click on the track, and go to Change Track Height (around 500 works fine).

That's pretty much it. You can see links between regions with curves. That said, it does not look great. Basically because this feature is usually used to visualize exon coverage for RNA-seq experiments.

I would personally recommend setting up a JBrowse instance, and install the Plugin SashimiPlot