Interpreting splice junctions on IGV
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3.0 years ago
jojorama • 0

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 • 1.5k views
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3.0 years ago

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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