rhysf
commented
3 weeks ago Hi @pcampiteli Plots look quite nice.
You should be able to subset the .coords and .coords.spans files to just the genes or gene regions of interest, in your case, either the core or the auxillary genes.
Then, I think your best bet is to edit the config file directly, and provide the location of those new files you've made, and choose a color... that should allow you to have 2 different colors for the syntenic lines depending on your category.
Hope that helps, Rhys
Greetings I'm running a syteny analysis on multiple genomes.
Context: I'm studying the overall synteny among multiple assemblies of a eukaryotic organism, First I took 1 assembly of each species and runned the orthofinder analysis to identify the core genome. Now I want to use this core genome infor, to inspect the core genomes synteny on intra-specific levels, for species with more than 2 genomes assemblies.
In the following exemples I could color the gene set using the parameter -k and -l.
Example one: I took the gene IDs from the species I used to identify the core genome and inputted as -k parameter
The result is good, But I'm interested in coloring the correspondence orthology among the subjected species
Example two, I filtered the IDs based on the orthogroups that included the core_genome_ids, creating a list with the core_genome of all orthologs, and a accessory_genome with the orthogroups not represented in the core_genome.
In this step I could color the line with specific color, but It did not was colored based on the core and accessory genomes.
So, My question is, is there a way to color the synteny lines based on the specific gene set used? Thanks in advance