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Old 03-18-2014, 01:49 PM   #1
blakeoft
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Default Potentially basic question involving IGV

I'm sorry for asking a potentially basic question, but can anyone tell me what the direction of the arrows indicates in the picture?
These are two genes taken from somewhere in chromosome 17 of the human reference hg19, being observed by IGV.
Thank you.

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Old 03-18-2014, 01:50 PM   #2
ECO
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Direction (and thus strand) of transcription.
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Old 03-28-2014, 06:26 AM   #3
blakeoft
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Thank you for your reply. I have another question. What does a red variant mean on IGV? I read through the online document about VCF files here http://www.broadinstitute.org/igv/viewing_vcf_files, but it only mentions what dark blue, cyan and grey mean. Also, what does it mean if a variant has multiple colors? In my picture, I have two calls with dark blue over red.

Here is an example.

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