I'm trying to get an image of my alignment in IGV, but I keep getting these blue lines that span my individual reads. Do you know what they are and how to get rid of them?
example image is here: https://ibb.co/Ybn4vTj
How to add images to a Biostars post
They are spliced reads, but I think you have to remove them from the bam/bed, I am not sure if there is a faster method or if you can do this with IGV tools.
They are spliced junctions.
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