Full genome phyloP scores from UCSC Browser

Question

[cetin.m]

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!!

Answer 1

[Alex Reynolds]

A: Retrieving Phylop Scores Using R

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

Answer 2

[cmdcolin]

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