Sashimi plot not generating

[Donna Leet]

Hello, 

I was provided with a bulkRNAseq .bam and .bai file from my collaborator labeled as such: Aligned.sortedByCoord.duplicateRemoved.withReadGroups.Split.bam; Aligned.sortedByCoord.duplicateRemoved.withReadGroups.Split.bam.bai. I am able to load them into IGV with the GRch38 genome but when I select "Show Splice Junction Track", nothing shows up as below. Similarly, no Sashimi plot is generated. I have selected RNA as Experiment Type. What could be going on?

Sashimi plot:

[igv-help]

I don't see any split alignments in your screenshot,  that is to say there are no connecting lines between the gray alignment blocks.     So there is no splicing information to display.   A typical RNA-Seq dataset will look like the screenshot below, note the many connecting lines between alignments.

This could be due to the options used during the alignment step.