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MM39 BED Files Genome Features

Hi All,

Is there some place where I can find BED files for genome features from the mouse mm39 genome build? Would like as many genome features as possible. Promoters, enhancers, CpG islands, etc....

Would pulling them off the UCSC genome browser be the way to go if they don't already exist somewhere?

Best,

Joe

bed mm39
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updated by GenoMax GenoMax • written by joseph.landry • joseph.landry

Have you looked at the data available on Jackson Lab's MGI?

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written by Ram Ram

Promoters are usually approximated as -500bp upstream of a transcription start site, so this you can easily parse from any GTF file, say from ENCODE for mm39. The other features, so enhancers, CpG islands, are all highly celltype-specific so there is not one single resource to simply get them from. Can you elaborate more?

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written by ATpoint ATpoint

One option is to get the bigBED file from UCSC here --> https://hgdownload.soe.ucsc.edu/gbdb/mm39/gencode/gencodeVM38.bb

Convert it to BED format using bigBedToBed utility found here --> https://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigBedToBed (linux version linked, macOS available). Make the file executable after download by doing chmod +x bigBedToBed.

./bigBedToBed gencodeVM38.bb gencodeVM38.bed

Enhancer bigBED file is here (convert to BED as above) --> https://hgdownload.soe.ucsc.edu/gbdb/mm39/vistaEnhancers/vistaEnhancers.bb

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written by GenoMax GenoMax

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