match CpG positions to genes

Question

[Pin.Bioinf]

Hello, I want to map the CpGs I have to their correspondant genes. I have the following information:

chr     CpG_position     sample1        sample2    ...
1            1058335       .....          ....
1            1058345       .....          ....
3              ....        .....          ....

How can I map those cpgs to a gene name if I only know that hg37 has been used? They are TAB seq and BS seq results (EPIC)

Answer 1

[Devon Ryan]

bedtools intersect or bedtools annotate would come to mind. Download or make a BED file with the bounds of genes to use with that.