Defining the genomic context given a genomic position
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3.5 years ago
mike ▴ 50

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!

RNA-Seq exon intro enhancer promoter • 948 views
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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.

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3.5 years ago

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.

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Awesome! Thank you very much.

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