Question: Blue line in Alignment track of IGV
0
gravatar for mb314
6 months ago by
mb3140
mb3140 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 • 195 views
ADD COMMENTlink modified 6 months ago by Buffo1.7k • written 6 months ago by mb3140

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

ADD REPLYlink written 6 months ago by mb3140

How to add images to a Biostars post

ADD REPLYlink written 6 months ago by WouterDeCoster41k

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 6 months ago • written 6 months ago by Buffo1.7k
1
gravatar for Buffo
6 months ago by
Buffo1.7k
Buffo1.7k wrote:

They are spliced junctions.

ADD COMMENTlink written 6 months ago by Buffo1.7k
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