Qustion about Circos Plot
Entering edit mode
3.3 years ago

Hello everyone,

I have some questions about the legend of the Circos graph: This is the plot I see

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

Circos • 592 views
Entering edit mode

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?


Login before adding your answer.

Traffic: 2148 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6