A question regarding phyloP conservation scores !

[Rubayte Rahman]

Dear Sir,

The WigFix format for PhastCons are given in this way:


fixedStep -- keyword indicating the wiggle track format used to write the data. In fixed step format, the data is single-column with a fixed interval between values.
chrom -- chromosome or scaffold on which first value is located.
start -- position of first value on chromosome or scaffold specified by chrom. NOTE: Unlike most Genome Browser coordinates, these are one-based.
step -- size of the interval (in bases) between values.


I want to know that, the scores for phyloP in WigFix format are supposed to be treated in the same fashion as stated above?
I looked in the README file for the phyloP scores in the ftp but the link for the description of the data file is redirecting to a different page.

here is the link in the README for the phyloP data description file : http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cons46way


Thanks in advance,
Rubayte Rahman

[Brooke Rhead]

Hi Rubayte,

The PhastCons scores for the 46-way multiple alignment are indeed in
fixedStep wiggle format. Looking at the beginning of each file will
confirm this. For example, the chrX.phastCons46way.primates.wigFix.gz
file begins with:

fixedStep chrom=chrX start=60546 step=1
0.210
0.207
0.203
0.198
0.193
0.187
0.181
0.174
0.180

A longer description of the wiggle fixedStep format is here:

http://genome.ucsc.edu/goldenPath/help/wiggle.html

If you have further questions, please contact us again at
gen...@soe.ucsc.edu.

--
Brooke Rhead
UCSC Genome Bioinformatics Group