Gene Annotation in Bed file

Question

[rah]

Hi All,

I'm currently working with a bunch of bed files containing specific regions of the human genome.

I wish to annotate the regions with genes, and especially genes related to man. However, to do this, I need a bedfile with the coordinates for each gene and a proper naming for that gene in order to perform bedtools intersect.

I know i gain the identification of the different genes on the http://genome.ucsc.edu/cgi-bin/hgTables, but do any of you guys know a proper database containing the disease-related genes with their corresponding coordinates?

Thanks for your time

[steve]

I have some different scripts for annotating .bed files listed here: https://github.com/stevekm/annotate-peaks These should include instructions on how to get the required reference data. However these days, I tend to prefer using VEP if possible. The official docs have plenty of instructions though I also have an example workflow here; https://github.com/stevekm/vep-annotation-nf . Also I have some scripts here that build some reference files which might be useful; https://github.com/stevekm/reference-annotations

Answer 1

[Haci]

For disease related genes you might want to check OMIM. You would need to register to download data. For the gene coordinates, there are a few repos, Ensembl, UCSC. As far as I remember, you would need to retrieve gff (or) gtf from Ensembl and than convert to bed format. UCSC Table Browser enables to download data in bed format.

[Luis Nassar]

As Haci mentioned, OMIM is a good source of disease data. I wanted to note you can access it from UCSC (http://genome.ucsc.edu/cgi-bin/hgTables) under:

Group: Phenotype and Literature Track: OMIM Alleles

But due to data restrictions, can only query one chromosome at a time.