GERP scores

[Niyati Jain]

Hello,

I want to compute base-wise GERP scores for a large set of genes. I have previously used the web table browser to extract the base-wise scores for defined genomic coordinates and then computed average GERP scores per gene using bedtools. 

I believe there is a limit on the number of lines in the output file when using the web table browser, and since I want to query a lot more genes this time, I was wondering what would be the best way would be to extract GERP scores.

Best,

Niyati

 

[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending your inquiry.

You can download the underlying tables and data files for your assembly from the downloads server. Please note that some track data is stored in each assembly's /gbdb directory:

http://hgdownload.soe.ucsc.edu/downloads.html
http://hgdownload.soe.ucsc.edu/gbdb/

You may be happy to know that Ensembl has whole-genome GERP scores available at:

https://ftp.ensembl.org/pub/current_compara/conservation_scores/.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro

UCSC Genome Browser

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