How to plot reads in IGV?

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Tiffany G

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Oct 31, 2023, 9:29:34 PM10/31/23
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I made a bed file with columns containing chr, start, end but when I loaded the file into IGV I got a 2D plot that looked like refgenes instead of mapped reads and composite peaks (i.e. a normal ChIP track). How do I get it to look like a histogram/ChIP track? What are the necessary information to include.


Screen Shot 2023-10-31 at 8.26.41 PM.png

igv-help

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Nov 1, 2023, 9:47:39 AM11/1/23
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That is how .bed files are displayed. 
The following file formats can be displayed as bar charts: .bedGraph, wig, bigWig, tdf.  
If you want to display mapped reads along with a coverage chart, you need to load a .bam or .cram file.
You can see more about file formats that IGV accepts here: https://igv.org/doc/desktop/#FileFormats/DataTracks/

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