Where can I find a hg19 genome annotation file?

[Heisman]

I've been looking around and searching a bit and can't find anything definitive. Basically I have a long list of genomic regions corresponding to called peaks and I would like to annotate these regions (ie, say X amount are in genes, promoter regions, exons, intergenic, etc). I'd like to download a file with all of the gene coordinates and if possible other information as well (promoters, exon/intron boundaries, etc) so I can do this. This link probably has what I need but there are so many files I'm not sure how to go through them all to figure it out: http://hgdownload.cse.ucsc.edu/golde...hg19/database/

Are there any well established files available for download that are typically used for annotating genomic regions?

[dpryan]

It's easier to use the table browser and export knownGene as a GTF file.

[Heisman]

Thanks, that could be useful. I also found this: http://www.gencodegenes.org/releases/17.html

http://epiexplorer.mpi-inf.mpg.de/ looks useful as well.

[GenoMax]

You could visit the iGenomes site and get it from the (albeit) large download.

OR save some electrons and get it from

From NCBI: ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/GFF/

[Heisman]

Very nice, thanks!

Edit: wow, that file is 20 GB compressed... what does it actually contain to make it so large?

[GenoMax]

Very nice, thanks!

Edit: wow, that file is 20 GB compressed... what does it actually contain to make it so large?

It contains sequence, pre-built indexes for BWA, Bowtie, Bowtie2, Annotation.