Hi all,
I have a set of genes (n=120) from Arabidopsis. I want to find out and plot their distribution in 1-Mbp interval along the chromosomes. I need this information to generate a figure similar to the one in attached file- https://ibb.co/gCMRQc.
Can someone tell me how to do this? I'm new to the data analysis and trying very hard since last few days but couldn't complete the task. Any help would be appreciated.
Thanks!
2 answers
This post shows how to bin feature counts by chromosome intervals (substitute gene position file for VCF). Then use R (or even the dreaded Excel) to generate the plot.
You can use the USCS Genome Browser and the Genome Graphs tool to upload your gene annotations (and their positions), and render them over ideograms for your genome build of interest.
A Genome Graphs figure will look very much like what you linked in your question.
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Thank you guys! I will look into the post/links..