Question: Full genome phyloP scores from UCSC Browser
1
gravatar for cetin.m
2.1 years ago by
cetin.m50
cetin.m50 wrote:

Hi,

I need phyloP scpres for the whole human genome. I was able to download 10M positions from http://genome.ucsc.edu/cgi-bin/hgTables using these instructions:

group: Comparative Genomics

track: Conservation

table: your phyloP table of choice

region: genome

output format: data points

However I need the whole genome information, not just 10M.

The website directs me to the downloads page, but I was lost there unfortunately.

Can anyone please link me to the correct place? (Human Grch37 phyloP values in data point format)

Thanks!!

ucsc database • 2.0k views
ADD COMMENTlink modified 2.1 years ago by cmdcolin1.5k • written 2.1 years ago by cetin.m50
2
gravatar for Alex Reynolds
2.1 years ago by
Alex Reynolds31k
Seattle, WA USA
Alex Reynolds31k wrote:

A: Retrieving Phylop Scores Using R

A: How to I automate getting a conservation score from UCSC if I have exon coordina

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by Alex Reynolds31k
1
gravatar for cmdcolin
2.1 years ago by
cmdcolin1.5k
United States
cmdcolin1.5k wrote:

A bigwig file for phyloP on hg19 whole genome is here http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP100way/

It's a large 8.9Gb bigwig so I do not necessarily suggest converting this into text format all at once, but you could convert to text using bigWigToBedGraph (or convert small chunks at a time with this tool, which accepts -chrom, -start, and -end arguments)

http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bigWigToBedGraph

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by cmdcolin1.5k
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