From base pair position to gene name to epigenetics

Question

[blue.dot]

Hello, I would like to preface that I'm new to bioinformatics and teaching myself.

I have a file containing hypermethylation data with the following: chromosome,start,end An example line would be: chr1,8882206,8882207

How do I take this one base and find its gene name? Specifically what file gives me the start and end positions for all the genes of an organism? I will be using the gene name from each line to find what the function of each position is. From there I will try to quantify what functional changes hypermethylation had on the organism.

Much thanks, sorry if this is a simple question.

Answer 1

[Devon Ryan]

You can download genes and their locations for many many popular organisms via biomart. You'll have to modify the results to get them into BED format, after which you can use either bedtools closest or bedtools intersect.