Interpreting splice junctions on IGV

Question

[jojorama]

I am currently analyzing some RNA-seq data. I am using STAR for my alignment and am looking for a particular type of isoform.

I uploaded the BAM FIles on IGV and the results look like this:

I am not sure why the splice junction tract looks symmetric. Is this an error? Furthermore my gene goes from right to left.

Thanks!

Answer 1

[GouthamAtla]

I GUESS its showing splice junctions by strandedness of your reads. Thats why it looks symmetric. It doesn't matter if your gene goes left to right or right to left.