Recombination hotspots hg38

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Dhupal Patel

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Jul 6, 2021, 2:17:54 PMJul 6
to gen...@soe.ucsc.edu

Hi,

 

Please could I have some help in finding and downloading the recombination hotspots for hg38?

 

Thanks,

Dhupal

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Dan Schmelter

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Jul 7, 2021, 3:00:58 PMJul 7
to Dhupal Patel, gen...@soe.ucsc.edu

Hello Dhupal,

Thank you for your question about finding recombination data.

We have two resources related to recombination hotspots, but they are on the hg19 reference genome. To convert them to hg38, you will have to download the data and use the LiftOver tool.

http://genome.ucsc.edu/cgi-bin/hgLiftOver

The hg19 datasets are "Recombination Rate", which has data from three separate experiments.

https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=recombRate

You can download it in its entirety from our Downloads server:

https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/recombRate.txt.gz

Or you can use our Table Browser tool to chose which fields to include or exclude, for example, you may only want the chr, start, end, and three averages columns.

https://genome.ucsc.edu/cgi-bin/hgTables?db=hg19

There is another dataset that includes more deCode recombination rates as well as HapMap Recombination rates. It is also on hg19, so you may want to convert that to the hg38 genome coordinates. The data is in "bigWig" format, which must be converted into bedGraph (with Table Browser for <100k regions or a command-line utility for the whole file) before inputting into LiftOver. You can read the description and download the data with the following links:

https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=decodeRmap
https://hgdownload.soe.ucsc.edu/gbdb/hg19/decode

I hope this was helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Kindly,
Daniel Schmelter
UCSC Genomics Institute


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