Obtaining PhyloP Scores

[Maxim Y Wolf]

Hello,

I'm trying to download the conservation scores (phyloP) for a specific set of regions defined by a custom file in bed format (in hg19).

Is there a way to obtain those values using the table browser without downloading the entire genomic alignment that is part of the phyloP100way track and then parsing it to find the scores.

I'm looking for just the conservation score in about 30000 short 100bp regions.

Thanks for any help on the matter.

Cheers,

-Max

[Matthew Speir]

Hello, Max.

Thank you for your question about obtaining PhyloP conversation scores for a set of regions from the UCSC Genome Browser.

This can be done using the Table Browser, https://genome.ucsc.edu/cgi-bin/hgTables, and a BED custom track of your regions. Use these steps to get your desired output:

1. Upload regions as a custom track:

1. Navigate to the custom track upload page: https://genome.ucsc.edu/cgi-bin/hgCustom?db=hg19.
2. Paste your custom track data in the box below "Paste URLs or data".
3. Click 'submit'.
4. Select 'Table Browser' from the drop-down menu.
5. Click 'go'.

2. Intersect custom track with PhyloP track:

1. Navigate to the Table Browser, https://genome.ucsc.edu/cgi-bin/hgTables.
2. Make the following selections:
• clade: Mammal
• genome: Human
• assembly: Feb. 2009 (GRCh37/hg19)
• group: Comparative Genomics 
• track: Conservation
• table: 100 Vert. Cons (phyloP100wayAll)
• region: genome
• output format: data points
• output file: (input a name, or leave blank to view results in your web browser)
3. Next to 'filter', click 'create'.
4. From the drop-down menu next to 'Limit data output to', select '10,000,000'.
5. Click 'submit'.
6. Next to 'intersection', click 'create'.
7. Make the following selections on the 'Intersect with phyloP100wayAll' page:
   
• group: Custom Tracks
• track: My Regions
• table: my_regions
• Select 'All phyloP100wayAll records that have any overlap with My Regions' 
8. Click 'submit'.
9. Click 'get output'.

After following these steps, you should have a fil with output that looks like this for your regions:

variableStep chrom=chr21 span=1
33031597	0.213748
33031598	0.119803
33031599	0.777417
33031600	-0.162032
33031601	-0.443866

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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Matthew Speir

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