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Question: How Do I Get A Phylop Input File?
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gravatar for Stephanhart
9.3 years ago by
Stephanhart • 100
Stephanhart • 100 wrote:

I would like to find conservation scores between a limited number of primate species for a protein-coding gene. As I understand it, the phyloP input file looks like this:

chr22 16440426 14440427 C/T

Starting with an Ensembl ID for my gene, how can I generate this type of file. Any help is appreciated.

Thanks Stephan
format file • 2.1k views
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modified 7.5 years ago by spacemorrissey • 240 • written 9.3 years ago by Stephanhart • 100
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gravatar for spacemorrissey
7.5 years ago by
spacemorrissey • 240
United States
spacemorrissey • 240 wrote:

I am not completely clear on what you want, but if you are looking for the conservation score across a gene or a group of genes, you can simply look up the location of the gene. Once you have the chrom, start, and stop in bed format, you can download the PhyloP bigwig track from the UCSC browser and use BigwigAverageOverBed to get the score across the gene, or list of genes.
ADD COMMENT • link written 7.5 years ago by spacemorrissey • 240
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