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Download bigWig files of publicly available ChIP-seq samples

There are a couple of efforts to provide quality controls of publicly available ChIP-seq data sets (e.g. http://www.ngs-qc.org/ and CISTROME. But is there a way to obtain the normalized bigWig files? Cistrome, for example, allows you to explore the coverage data via UCSC or WashU, which means they definitely have the data, but it seems they only provide the BED files of peaks for download.

Is there a way to obtain normalized bigWig files of publicly available ChIP-seq samples? (other than [mod]ENCODE)

cistrome bigwig chip-seq
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written by Friederike Friederike

1 answer

Hi, I guess it depends ! For CISTROME, you can obtain them by clicking on the UCSC link to open a genome browser page -> click on the track name below the browser windows in the Cistrome Analysis Hub section -> click on view table schema -> copy link for bigwig file.

For other ChIP-seq (raw) data submitted on GEO, there are often bigwigs files posted along as supplementary data, so it is also a good source for bigwigs.

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written by Carlo Yague Carlo Yague

UCSC link to open a genome browser page -> click on the track name below the browser windows in the Cistrome Analysis Hub section -> click on view table schema -> copy link for bigwig file.

That's nifty, thanks!

For other ChIP-seq (raw) data submitted on GEO, there are often bigwigs files posted along as supplementary data, so it is also a good source for bigwigs.

That is true, but I am specifically looking for data from different labs (for, say, the same factor) that was normalized in the same way.

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written by Friederike Friederike

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