Question: Plot a Score for Several Genomic Regions
0
gravatar for fusion.slope
3.3 years ago by
fusion.slope210
fusion.slope210 wrote:

Hello,

am trying to plot for several genomic regions its respective score that i have calculated (with some assumptions). I have the bed file that looks like this.

Chr Start End Score
chr1 1 400 -3
chr1 5000 5400 +10

etc..

I would like to plot the score position for position.I checked this previous post (C: Plotting Density Of Snps On Chromosomes) but am not sure if in that way is totally correct. There the guys use density values of the SNPs and i have score values.

Thanks for any reply.

plot genomic regions score • 962 views
ADD COMMENTlink modified 3.3 years ago by Alex Reynolds30k • written 3.3 years ago by fusion.slope210
1

The easiest way would be to convert that (it's a bedGraph file) into a bigWig, load it into IGV and save that as an image.

ADD REPLYlink written 3.3 years ago by Devon Ryan95k
2
gravatar for Alex Reynolds
3.3 years ago by
Alex Reynolds30k
Seattle, WA USA
Alex Reynolds30k wrote:

To visualize, perhaps look into preparing a custom track on the UCSC Genome Browser, importing your tab-delimited Bedgraph file. Numbers are numbers.

Once you have added your custom track, you can use the Genome Graphs functionality to visualize it on chromosome ideographs (you can also visualize other signals with the same tool) and use the View > PDF menu option to export a PDF file.

enter image description here

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by Alex Reynolds30k
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