Visualizing my RNAseq data, I find many instances of multiple sashimis stretching over the same inton, see for example: https://i.imgur.com/rEK7bQM.png

Is this a bug? If not, is there a way to combine those into one sashimi?

It is not a bug. I guess, that the reads do not start at exactly same position. You can use argument sashimiFilterTolerance and set it to small integer (5L) to merge those into one arc. It is describe in the vignette.

Best

Robert

I figured out the problem.

It was not the missing sashimiFilterTolerance argument (which I used already), but the introns specified in the sashimiFilter argument. It contained the same intron multiple times and I suppose GViz draws a sashimi for each specified intron, if there are reads stretching over this intron.

Best,

Frederik