display a count numbers as bar chart

[Fred Shaw]

I have a BED file like

chr1 23768 24500 10

chr1 30000  35000 5

The last column has copy counts. When I load this BED file into IGV. It shows the numbers in the last column as numbers (10. 5, etc.). Is there anyway to show them as bars in a bar chart, like the bar chart for gene expression data? But this file is not gene expression file, just some count.

Thanks,

Fred

[James Robinson]

You need to use a "bedgraph" file,  in "bed" format the 4th column is the feature name.   This is as simple as renaming the extension go "bedgraph" to indicate the format.

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[Fred Shaw]

Hi Jim,
Worked! Thank you.
One more question, is there a way for me to add all count numbers in 0.5 million base intervals into 1 number and display them in bar chart?
Thanks,
Fred

On Thursday, April 6, 2017 at 2:34:32 PM UTC-4, Jim Robinson wrote:

You need to use a "bedgraph" file,  in "bed" format the 4th column is the feature name.   This is as simple as renaming the extension go "bedgraph" to indicate the format.

On Thu, Apr 6, 2017 at 2:17 PM, Fred Shaw <fredn...@gmail.com> wrote:

I have a BED file like

chr1 23768 24500 10

chr1 30000  35000 5

The last column has copy counts. When I load this BED file into IGV. It shows the numbers in the last column as numbers (10. 5, etc.). Is there anyway to show them as bars in a bar chart, like the bar chart for gene expression data? But this file is not gene expression file, just some count.

Thanks,

Fred

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[James Robinson]

Not in IGV, you would need to write a script to compute that.

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[Fred Shaw]

Thanks.