Downloading ENCODE histone data in BED format

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Wilson, Gareth

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Aug 30, 2012, 10:37:16 AM8/30/12

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Hello,

I'm trying to download several encode datasets, for example wgEncodeBroadHistoneGm12878H3k27acStdSig for human build hg19. From the 'Table Browser', I can select to download the file in bed format, however I am limited to just a few thousand lines (having increased the filter to 10,000,000). I searched for an equivalent file in the 'Download' section but could only find a txt file containing a single line displaying the path to a bigwig file. Using this path, I accessed the ftp site, hoping to find the full bed file – unfortunately I could only find bigwig files. Potentially I could download the bigwig file and convert to bedGraph but this isn't the bed format I'm after! I think I must be missing something somewhere!

How can I download these ENCODE datasets in BED format?

Many Thanks,

Gareth.

Pauline Fujita

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Sep 6, 2012, 9:25:57 PM9/6/12

to Wilson, Gareth, gen...@soe.ucsc.edu

Hello Gareth,

For BED ENCODE files, you will need to download the 'peak calls' which
are in the extended BED ENCODE formats -- broadPeak or narrowPeak.
These formats are described here:

http://genome.ucsc.edu/FAQ/FAQformat.html#ENCODE

For example, the dataset you mention (H3K27ac histone mark in GM12878
cells) has a BED file representation in the file:

wgEncodeBroadHistoneGm12878H3k27acStdPk.broadPeak.gz

It is available for download via FTP. You can find this and other
related files using our "File Search tool" here:

http://www.genome.ucsc.edu/ENCODE/search.html

i.e. on hg19, if you go click on File Search and choose:

Data Format: Peaks Broad
Cell, Tissue or DNA Sample: GM12878
Antibody or Target Protein: H3K27ac

You should see the file you are looking for as well as a reference to
the downloads directory housing related files:

http://www.genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeBroadHistone

Hopefully resolves your issue. If you have further questions please
feel free to contact the mailing list again at gen...@soe.ucsc.edu.

Best regards,

Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu