Discrepancy between Genome Browser hg19 phyloP Score and that of wig data
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3.2 years ago
progistar ▴ 40

Hello,

I'm starting conservation analysis with phyloP score by UCSC Genome Browser. They provide phyloP score here: "http://hgdownload.soe.ucsc.edu/goldenPath/hg19/phyloP100way/" However, the score is a little bit different from that of score seen by UCSC Genome Browser. For example, a position chr6:46721460 in the Genome Broswer is denoted as 0.0046... but in the wig data (you can download via the above link) the same position has a value of 0.035. Of course, the discrepancy between them is not much big (maybe it can be acceptable to determine conserved region... in my thought); I still want to know the reason why.

If there is anybody knows about it, please reply.

Thanks for your attention.

phyloP genome browser • 778 views
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Hi,

I think UCSC Genome Browser uses this file here.

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Thanks for your reply. I checked the file up and thought that the file records phyloP score by 1024 positions as a block. To compare easily, I want to access single position phyloP score... could you let me know the origin source (URL)?

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