Downloading ENCODE regulation data in .bed format by cell line
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6.9 years ago
drautuna ▴ 60

So, I have a list of variants I want to annotate based off several databases in .bed format. The rest of the databases I want to include are off of ENCODE, but despite my searches I cannot for the love of my life download the data off ENCODE based off cell line.

I always end up at this page, which provides me ALL the databases, but not by cell line. I found a search function here, but for some reason, whenever I run a search, it doesn't return any results.

I am looking for .bed files listing sites of DNA methylation, DNase-seq, Chip seq (TFBS and histone modifications) for HepG2, K562, GM12878, and Human Skeletal Muscle cell lines each.

I am basically asking: How can I get these off ENCODE? Thanks.

cell BED ENCODE databases annotations line • 5.4k views
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6.9 years ago
komal.rathi ★ 3.9k

You go to the Encode Data Matrix for hg19 -> Click on the green boxes -> You will see a lot of tracks under the column name Track Name -> There is a small arrow at the end of the tracks which will expand the track, click on it -> You will get the links to narrowpeaks.bed.gz or broadpeaks.bed.gz which you can directly download. You might not get every data that you need though.

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Thank you for the nearly instantaneous reply! Saved me a lot of time looking where to download the databases

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Actually, I have a quick followup question: How can one download all of the chip-seq data quickly? It is extraordinarily tedious to download each of the hundred histone modificiation and TFBS files one by one

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You can use this linkto download the data. Follow these instructions.

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6.9 years ago
onuralp ▴ 190

If you are interested in BigBed files by data type, here is a link to fdrPeaks as a pointer: fdrPeaks.bb I think the link address is informative as to explore similar datasets.

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