Whole Genome View Colors in BED

[Jennifer Hauenstein]

I am trying to show copy number data in a BED format in IGV. I can see the different colors I have denoted when I go to a particular chromosome but not when viewing the whole genome. How can I see my colors on the whole genome view?

Thank you~

Jen

[James Robinson]

Bed features are not displayed in whole-genome view,  rather the density of features.   Bed format support was designed for annotation features (like genes), not really for numeric data such as copy number.  

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[Jennifer Hauenstein]

Ok, thank you. Do you know anyway to show a whole gains and losses with different colors for the whole genome view? I have created bigwig files but they do not show the whole chromosome gained just a single peak for the abnormality.

On Saturday, June 3, 2017 at 5:11:57 PM UTC-4, Jim Robinson wrote:

Bed features are not displayed in whole-genome view,  rather the density of features.   Bed format support was designed for annotation features (like genes), not really for numeric data such as copy number.  

On Sat, Jun 3, 2017 at 1:10 PM, Jennifer Hauenstein <jenhaue...@gmail.com> wrote:

I am trying to show copy number data in a BED format in IGV. I can see the different colors I have denoted when I go to a particular chromosome but not when viewing the whole genome. How can I see my colors on the whole genome view?

Thank you~

Jen

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[James Robinson]

Not at this time. 

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[James Robinson]

I mean not at the present time for the "bed" format.  Do you want to choose your own colors?  The standard format for this is the ".seg" format,  but it will display colors based on numeric value.    See http://software.broadinstitute.org/software/igv/SEG

The standard heatmap is red-blue,    you can change this with a track line.  See http://software.broadinstitute.org/software/igv/TrackLine,  specifically color (+ values),  and altColor (- values),  and viewLimits to set upper and lower bounds.    Optionally you can set midRange and midColor.  

[Jennifer Hauenstein]

James!

Thank you so much for your help!!! This is EXACTLY the direction I needed! I am soooooo grateful.

Jen

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