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Published 20 hours ago • verified publisher icon JustinChu

Set links between chromosomes

Open Karimi-81 opened this issue 3 years ago • 1 comments

Hi there, I used the JupiterPlot to present the synteny between two genomes using default parameters: ./jupiter name=genome_two ref="polished_assembly.fa" fa="C_1.0_genomic.fna" t=32 ng=75

Attached is the circos plot generated. I wonder how can I change the color and thickness of links (I want wider links) between chromosomes. In addition, how it is possible to add the names of scaffolds (or chromosomes) to second genome (right hand side of image). Regards circos_2

Karimi-81 avatar May 23 '21 01:05 Karimi-81

Sorry if this reply is too late. To create wider links you could try to change the parameters minBundleSize (decrease) and maxGap (increase) which will allow larger gaps when between aligned regions. Any additional changes will require development probably tweaking filtering and mapping parameters.

JustinChu avatar Oct 22 '22 03:10 JustinChu

Stale issue. Closing.

JustinChu avatar Apr 05 '24 01:04 JustinChu