Database for Enhancers with Coordinates
Can anyone recommend some good databases for extracting bed files with enhancer coordinates. I have used UCSC in the past, I was hoping to find some alternatives
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There is Ensembl's too.
Here is information on it: https://useast.ensembl.org/info/genome/funcgen/regulatory_build.html
You could find the previous annotations here through some clicking:
If you want to use GRCh38:
You could download, gunzip, then do something like:
grep Enhancer homo_sapiens.GRCh38.Regulatory_Build.regulatory_features.20210107.gff | cut -f1,4,5 | awk -F "\t" '{ print "chr" $1,$2,$3 }'
There is also https://screen.encodeproject.org/ which I think Ensembl uses to curate their regulatory build file above.
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Also check EnhancerAtlas, apart from coordinates it provides predictions for enhancer-gene target interactions, which may be useful.
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