Question

IGV empty tracks render in blue

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5.7 years ago

roy.granit ▴ 880

I'm using IGV to display CNV data, and for some tracks there are no CNVs.. but for some reason IGV renders these 'empty' tracks in blue..

Any suggestions on how to force IGV to color these in White?

Thanks

CNV IGV • 1.9k views

ADD COMMENT • link updated 5.5 years ago by Jim Robinson ▴ 300 • written 5.7 years ago by roy.granit ▴ 880

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Please show a screenshot and give some details on what file format you loaded into CNV.

ADD REPLY • link 5.7 years ago by ATpoint 81k

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Here is the image..

ADD REPLY • link 5.7 years ago by roy.granit ▴ 880

score 0 · Answer 1 · 2018-10-05

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5.5 years ago

Jim Robinson ▴ 300

Are these segmented copy number files? How did you determine that there are no CNVs on the tracks with blue bars. The blue bar indicates a CN < 2.

ADD COMMENT • link 5.5 years ago by Jim Robinson ▴ 300

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Yes, these are segmented CNVs detected using QDNAseq, I know there are no CNVs on the blue tracks by looking at the raw SEG files

ADD REPLY • link 5.5 years ago by roy.granit ▴ 880