[Genome] phastcons_scores

[Kayla Smith]

Hello Vlad,

Thanks for your compliments on the Genome Browser.

You are correct about the browser view you have supplied.  The value of 
hg18.phastcons at that position is close to 1 at the coordinate 
chr6:26195725.  The problem you're having is from looking at the wrong 
part of the associated file.

One of our developers here has suggested that you use the wigEncode 
program to get the following results:

% wigEncode chr6.pp.gz chr6.wig chr6.wib
% hgWiggle -position=chr6:26195715-26195740 chr6.wig
# output date: 2007-09-17 17:12:25 UTC
# chrom specified: chr6
# position specified: 26195715-26195740
# This data has been compressed with a minor loss in resolution.
# (Worst case: 0.00760156) The original source data
# (before querying and compression) is available at
# http://hgdownload.cse.ucsc.edu/downloads.html
variableStep chrom=chr6 span=1
26195714 0
26195715 0
26195716 0
26195717 0
26195718 0
26195719 0.0612913
26195720 0.114921
26195721 0.306457
26195722 0.444362
26195723 0.842756
26195724 0.91937
26195725 0.950016
26195726 0.965339
26195727 0.965339
26195728 0.965339
26195729 0.881063
26195730 0.835095
26195731 0.804449
26195732 0.697189
26195733 0.620575
26195734 0.367748
26195735 0.16089
26195736 0.10726
26195737 0.091937
26195738 0.122583
26195739 0.137906

I hope this is helpful to you.  Please don't hesitate to contact us 
again if you require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group

Vlad Babenko wrote:
>     Greetings,
>    First, thanks to UCSC developers for the work and assistance ;-)
>      Next is a problem:
> I didn't manage to coordinate hg18.phastcons tracks to that I may see in the browser. For example, it could be seen that the score =1 for the chr6 pos 26195725 (http://www.genome.ucsc.edu/cgi-bin/hgTracks?position=chr6:26195715-26195740&db=hg18&ss=../trash/hgSs/hgSs_www_221b_95c6a0.pslx+../trash/hgSs/hgSs_www_221b_95c6a0.fa&hgsid=92639599)
> 
> Still I may see that in file (http://hgdownload.cse.ucsc.edu/goldenPath/hg18/phastCons28way/vertebrate/chr6.pp.gz) it is, though close to local maxmum , but not 1: score=0.233.
>      Are the conservation wiggles the processed versions of the phastcons ones, or I'm missing something? For the phastcons file mentioned above I started with the header offset 5001 and counted off the position.
>      Thank you,
>            Vlad
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome