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mummer4 / mummer

Mummer alignment tool
Artistic License 2.0
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Manually ordering contigs/chromosomes with mummerplot #193

Open kcl58759 opened 1 year ago

kcl58759 commented 1 year ago

Hi, I would like to keep chromosomes of one of my genomes in the alignment in their original order but even with the -Q and -R options mummer seems to be coming up with its own order. Does anyone know how to fix this?

gematakbir commented 1 year ago

Hey, were you able to solve the issue? I also have this problem where my chromosomes were randomly ordered so the alignment do not look good. Please let me know if you have any solutions.

kcl58759 commented 1 year ago

Not with mummer. I ended up using dotplotly and that worked! https://github.com/tpoorten/dotPlotly/blob/master/mummerCoordsDotPlotly.R