Using phastCons30way in UCSC table browser

Question

[Aishwarya Kulkarni]

Hi,

I need to check phastcon score using phastCons30way track for a single conserved region and I want to check it in table browser, but I do not see the option to use the track in table browser, is there a way to do so?

[Ram]

Does this track even exist? I see only 46way and 100way (for hg19). If it doesn't exist, you'll have to create a custom track. If it does, adding it should be pretty straightforward.

[Aishwarya Kulkarni]

Hi I checked and 30 way phastcon is the track used to be compared against mouse genome.

[Ashutosh Pandey]

Assuming that your genome of interest is 'Human'

Go to Table Browser

Select 1) genome as 'Human' 2) group as 'Comparative Genomics' 3) track as 'Conservation' 4) table as 'phastCons100way' 5) enter coordinates for your region of interest in position 6) Select the output format and click on get output

Link:http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=448739083_YoLcEefvkocBcd7WIvpogImKURta&clade=mammal&org=Human&db=hg38&hgta_group=compGeno&hgta_track=cons100way&hgta_table=phastCons100way&hgta_regionType=genome&position=chr9%3A133252000-133252200&hgta_outputType=wigData&hgta_outFileName=

Answer 1

[Ram]

It's under mm9 > Comparative Genomics > Conservation > phastCons30way.

Given that you knew what organism you were working with (mouse) and the operation you were performing (conservation studies) that involved a particular type of processing (comparison), this should give you an idea on how to look for tracks in the table browser.