How to get human-mouse conservation score from UCSC
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7 weeks ago

Hello everyone,

I want to download conservation score data of human and mouse only from UCSC and then upload this data into IGV.

But I only get some information about conservation score at the Genome Browser or table Brower.

Though I found human related conservation score to other species here , hg38.phyloP4way.bw, this data contains four species and the size is huge.

This directory contains conversation scoring by phyloP (phylogenetic p-values) from the PHAST package (http://compgen.bscb.cornell.edu/phast/) for multiple alignments of 4 genomes to the Guinea pig genome.

*Files in this directory are:
    hg38.phyloP4way.mod  phyloP tree model with branch lengths
                        for the 5 genomes
    hg38.phyloP4way.wigFix.gz - phyloP scores for the 5 genomes
                                 in fixed step wiggle format
    hg38.phyloP4way.bw - phyloP scores for the 5 species
                          in bigWig format
    md5sum.txt - md5 sums of the files here to verify accurate download*

I am afraid that it is not easy to load into IGV. And it is not necessary to focus on other three species here.

So could somebody tell me where and how to get only conservation score data of human and mouse ?

Or another way to extract specific species conservation score from hg38.phyloP4way.bw ?

Thanks in advance.

conservation mouse IGV human score • 392 views
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Hello everyone,

I already know where to get hg38 versue mm10 convervation score information.

Just download it from https://hgdownload.soe.ucsc.edu/goldenPath/hg38/vsMm10/.

But new questions appear,

I want to have a look of conservation score in IGV, but this tool doesn't accept file formats like .maf, .chain or .net. For this case, I was wandering if one of these files of strange formats can be converted into .BED, .bw or .gtf formats ?

Could somebody give me some advice on my question.

Very thankful.

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Entering edit mode

Sorry for that here is wrong answer. This information is wrong and has nothing to do with conservation score.

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Please email UCSC browser support directly and post their answer. Folks from UCSC stop by here but not regularly.

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Thanks a lot.

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