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tanghaibao / jcvi

Python library to facilitate genome assembly, annotation, and comparative genomics
BSD 2-Clause "Simplified" License
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How to add telomere points on chromsomes? #339

Closed AlexWanghaoming closed 1 month ago

AlexWanghaoming commented 3 years ago

Dear developer, If I want to add telomere points on chromosomes rectangle in karyotype plot, what source code do I need to modify in jcvi.graphics? I have the position file of each telomere on both right and left of my chromosomes.

tanghaibao commented 3 years ago

@AlexWanghaoming

If it is in the karyotype plot then it is in this script: https://github.com/tanghaibao/jcvi/blob/main/jcvi/graphics/karyotype.py

This is interesting since I always assume the telomeres are on the exact ends of the chromosomes? or do you mean centromere positions? Would it be possible to sketch what you want?

AlexWanghaoming commented 3 years ago

Thanks for your reply. Sometimes the assemblies are not in chromosome level and we would like to use syntenic plot to judge whether two contigs are generated from actual chromosome breakage or failed assembly. Therefore, we have located telomere position on all of contigs and want to plot them on karyotype plot.