bam junctions

EMILIENE BERINYUY

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Nov 14, 2022, 4:11:30 AM11/14/22

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Hi Team,

I use IGV 2.13.2, I observed a bam junction after loading a bam file obtained from targeted DNA NGS sequencing. Please can you clarify what the bam junction signifies. Thanks.

igv-help

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Nov 15, 2022, 2:42:18 AM11/15/22

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We really need more information, I am unsure about what you mean by "bam junction". Perhaps a screenshot would help.

EMILIENE BERINYUY

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Nov 15, 2022, 2:52:18 AM11/15/22

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Please find below the screenshot. Just curious why the bam junctions on this file.

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Kind regards

Emiliene

Tata Emiliene Berinyuy

PhD fellow

Institute for Cellular and Molecular Medicine (ICMM)
Department of Immunology, University of Pretoria
Prinshof Campus, Pathology Building, Room 5-49
Telephone: +27(0)12 319 2101
Cellphone: +27(0)639782268

James Robinson

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Nov 15, 2022, 3:01:16 AM11/15/22

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I don't see any "junctions", what exactly are you referring to?

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EMILIENE BERINYUY

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Nov 15, 2022, 3:08:56 AM11/15/22

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The bam junction track was displayed for this file only thats what I was curious.

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James Robinson

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Nov 15, 2022, 3:19:40 AM11/15/22

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Oh, sorry, I misunderstood the question. That is set in your preferences. Select "View > Preferences > Alignments" tab and see if "Show Junctions Track" is checked. If it is not, check the "RNA" tab. Even though your data is DNA, it's possible IGV guessed wrong.

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James Robinson

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Nov 15, 2022, 3:20:29 AM11/15/22

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Also, you can always hide this track from the right-click menu. The option is near the bottom of the menu.

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