How to draw a Synteny map from coordinates file

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4.6 years ago

s_herrera ▴ 10

Hello,

I want to draw a Synteny map between a chromosome-level genome (reference) and a draft genome which is not assembled to chromosome level. I already have the output of SatsumaSynteny (satsuma_synteny.refined.out), which has the coordinates of the syntenic blocks, and looks like this:

chrX 5947 6164 chrX 9153 9360 0.626728 +

target start. end. query. start. end. identity. orientation

Unfortunately, I have not been able to use MizBee (http://www.cs.utah.edu/~miriah/mizbee/Overview.html) , which is the recommended browser that interfaces with Satsuma. Is there a way to draw the syntenic map just using the coordinates file using R or Python? Thank you in advance.

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synteny synteny map satsuma • 1.5k views

ADD COMMENT • link 4.6 years ago by s_herrera ▴ 10

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I am also unable to use MizBee - have you found a solution to this?

ADD REPLY • link 3.6 years ago by sophiematthews03 • 0

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Same here. I just get a blank screen when I try running the executable.. Any luck using circos or other programs?

ADD REPLY • link 3.5 years ago by pcvgt • 0

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