Genes on chromosome
Hello,
Is there a simple program where you can enter a set of genes (I have 10 genes). and then you get the location of the gene on the chromosome in one figure. So a figure with 22 chromosomes contains my gene of interest?
Many thanks, Fatma Mokhtar
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Check out the karyoploteR package - the
kpPlotMarkersfunctions looks useful. You'll need to use biomaRt or org.Hs.Eg.db to get coordinates for each gene.If you want to try karyoploteR, you can find a tutorial page with the code you need at https://bernatgel.github.io/karyoploter_tutorial//Examples/PlotGenes/PlotGenes.html
NCBI's genome data viewer may fit the bill (if your genome is on their list).
Drawing Chromosome Ideograms With Data
if it's a plant species you're working with you might have a look at PLAZA, especially the WGMapping tool: eg: https://bioinformatics.psb.ugent.be/plaza/versions/plaza_v4_5_dicots/genome_mapping/index