Question: Blue line in Alignment track of IGV
0
gravatar for mb314
16 months ago by
mb31410
mb31410 wrote:

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

igv • 473 views
ADD COMMENTlink modified 16 months ago by Buffo1.8k • written 16 months ago by mb31410

example image is here: https://ibb.co/Ybn4vTj

ADD REPLYlink written 16 months ago by mb31410

How to add images to a Biostars post

ADD REPLYlink written 16 months ago by WouterDeCoster44k

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 REPLYlink modified 16 months ago • written 16 months ago by Buffo1.8k
1
gravatar for Buffo
16 months ago by
Buffo1.8k
Buffo1.8k wrote:

They are spliced junctions.

ADD COMMENTlink written 16 months ago by Buffo1.8k
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