Question about PhasCons data via mysql

[Simon Fishilevich]

Dear UCSC team,

 

I am interested to retrieve data from the 100 vertebrates conservation by PhastCons track.

The UCSC mysql seems to return data per regions and not single genomic positions.

The table browser does allow such queries, using the ‘output format’=’data points’ option.

Can this be similarly done via mysql?

 

Best,

Simon

 

[Matthew Speir]

Hello, Simon.

Thank you for your question about getting PhastCons scores from the UCSC Genome Browser public MySQL server.

Yes, the phastCons tables do not contain the per base scores, but rather ranges and offsets into the "wib" file mentioned in the "file" column. This is done to help speed up the display of the data in the Genome Browser. 

However, you can download the original scores from our download server for hg19 and hg38 here:

• http://hgdownload.soe.ucsc.edu/goldenPath/hg19/phastCons100way/
  
• http://hgdownload.soe.ucsc.edu/goldenPath/hg38/phastCons100way/
  

For both of these, you can download a bigWig file of the scores, and then use our bigWigToBedGraph or bigWigToWig utilities to convert the bigWig file to a plain text format for local processing. You can download these utilities for your system type (Mac or Linux) here: http://hgdownload.soe.ucsc.edu/admin/exe/.

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.

Matthew Speir

UCSC Genome Bioinformatics Group

Training videos & resources: http://genome.ucsc.edu/training/index.html

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