Defining the genomic context given a genomic position

Question

[mike]

Hi all,

How can we find out the genomic context (genomic elements) given a genomic position (such as given a bed file).

Is the position in an intron or exon of a gene? If the position is intergenic : which gene are upstream and downstream (and distances) or maybe promoter, enhancer?

Are there maybe tools or R packages, python packages for doing this? Thank you!

[Pierre Lindenbaum]

see Defining Precisely The Genomic Context Based On A Position ; Is A Genome Position In An Exon Or Intron? ;

[ATpoint]

In addition, please use the search function and google. The keyword is 'annotation' of genomic regions. Plenty of posts on that available. If you need intron positions etc. based on a GTF file, see my tutorial.

Answer 1

[jared.andrews07]

The R package ChIPseeker does basically everything you want and is relatively easy to use. It'll also spit out some summary figures for you if you want them. Can also manually do this in R or python manually using biomart and a bit of thought if you wanted.

[mike]

Awesome! Thank you very much.