Question: Blue line in Alignment track of IGV
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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?IGV alignment

ADD COMMENTlinkeditmoderate 9 months ago mb314 • 0 • updated 9 months ago Buffo ♦ 1.6k
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example image is here: https://ibb.co/Ybn4vTj

ADD REPLYlinkeditmoderate 9 months ago
mb314
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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.

ADD REPLYlinkeditmoderate 9 months ago
Buffo
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They are spliced junctions.

ADD COMMENTlinkeditmoderate 9 months ago Buffo ♦ 1.6k

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