Manually ordering contigs/chromosomes with mummerplot

[kcl58759]

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]

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]

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