Plotting Genes on an arm of a Chromosome

Question

[maruthi]

Hi,

I have a list of SNPs which I want to use to design a bait for Target Sequencing for each arm of a chromosome. However, I am wondering now how would I know which genes are covered in each regions of the chromosome!

For example...

Chromosome num    Start           End               Num of SNPs
Chromosome 1           1          3000000 bp             85

How would I know which genes are actually in the above start and end region of the p arm of Chromosome 1 and how can I plot SNPs and genes together to show the information? Or is it a separate plot for SNPs and Genes!

I will look forward for suggestions.

Thank you,
Maruthi

[Irsan]

Do you just want to know how you can annotate a genomic interval (which is what you have) with gene symbols (e.g. TP53, RB1, E2F3) or do you want to do some plotting? Numerous questions and answers are available on biostars how to annotate genomic intervals, e.g. see here. If you want to plot/browse, the easiest way is to save your file as a tab-delimited file with .bedGraph suffix, then you can open it in IGV

[maruthi]

Dear Irsan,

Thank you for your suggestion. I want to annotate Irsan. I do not have any data from my NGS yet. I am still preparing a Bait. I have SNP data for each region (along with number of SNPs for a specific region) of the arm of a chromosome. However, I want to know which genes are in the regions, so I know the genes are going to be in the bait. I will have a look at the previous post you suggested. Please let me know if I am on the right track. This is my first NGS experience.

Thank you,

Maruthi.

[Irsan]

What is it you want to achieve in the end? Genotype polymorphism (SNPs)? Why don't you just use the baits in commercial whole-exome enrichment kits?

[zx8754]

For plotting look into ggbio package