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Interpreting splice junctions on IGV

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: enter image description here

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

Thanks!

rna-seq igv alignment sequencing
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updated by GouthamAtla 1.2K • | written by jojorama 0

1 answer

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.

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written by GouthamAtla 1.2K

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