GERP score bw files
Jinrui Xu
Hello ,
I found that under the directory of http://hgdownload-euro.soe.ucsc.edu/gbdb/hg38/dbNsfp/
There are two bw files
dbNsfpGerpNr.bw
dbNsfpGerpRs.bw
According to the file names, they seem the GERP scores of hg38 genome. However, which one of the file should be used?
Thanks!
Jinrui
Jairo Navarro Gonzalez
Hello,
Thank you for using the UCSC Genome Browser and sending your inquiry.
The dbNsfpGerpNr.bw file is the GERP++ neutral rate, and the dbNsfpGerpRs.bw file is the GERP++ "rejected substitutions" RS score. With both these files, the larger the score, the more conserved the site:
These scores are from dbNSFP, so they are for coding regions only and not the whole genome. You may be happy to know that Ensembl has whole-genome GERP scores available at:
https://ftp.ensembl.org/pub/current_compara/conservation_scores/.
More information about GERP scores can be found on the following articles:
Original GERP paper (explains concept of RS)
GERP++ paper (more rigorous algorithms for computing RS)
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
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Jairo Navarro
UCSC Genome Browser
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