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
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