Qustion about Circos Plot
Hello everyone,
I have some questions about the legend of the Circos graph:
It shows: The third ring represents indel density in scatter style. A black dot is calculated as indel number in a range of 1Mbp.
I wonder what is 'calculated as indel number in a range of 1Mbp'?
Many thanks, Aaron
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AaronZhanguk •
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I cannot see the image, but what I can understand from the text is that: 1 - You need to have the indels already computed and know the genomic position of each one 2 - Then, divide the genome into 1Mb windows (possibly overlapping) 3 - For each 1Mb region of your genome, count the number of indels you see in that region. 4 - Then you can optionally "normalize" that number dividing it by whatever you want: the maximum number of indels in a single 1Mb region, the total of indels in the sample... 5 - Each black dot represents that number for a 1Mb window and is plotted centered in the window
Does it make sense?