Phastcons Files

Question

[Pierre Lindenbaum]

I'm currently looking for the 'probability/score' of a base to be conserved threw the evolution. So I looked at the phastCons files at the UCSC.

I found a set of WIG files here:

• http://hgdownload.cse.ucsc.edu/goldenPath/hg18/phastCons44way

But there are also some (SQL) files here:

• http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/phastCons44way.txt.gz
• http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/phastConsElements44way.txt.gz
• http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/phastConsElements44wayPlacental.txt.gz
• http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/phastConsElements44wayPrimates.txt.gz http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/phyloP44wayAll.txt.gz
• (...)

what's the difference between those files ? Which source should I use ? Would you suggest another source of data ?

Many thanks

Pierre

[Animesh]

Hi ,

I am amso working with PhastCons files. Does the high scores means more conserved than the low score?

thanks

Answer 1

[Ning-Yi Shao]

If I am not wrong, they are different subsets of species that the PhastCon score method used to calculate the score. For the vertebrate.mod, even the coding regions may not be so conserved, while for the primates.mod, most regions--even non-coding regions are high conserved.

The txt.gz files contain information about lod score in bed formation (LOD=phastCons row log odds score). The further information you may check phastCon score program.

The program produces two main types of output. The primary
output, sent to stdout in fixed-step WIG format
(http://genome.ucsc.edu/goldenPath/help/wiggle.html), is a set of
base-by-base conservation scores. The score at each base is equal
to the posterior probability that that base was "generated" by the
conserved state of the phylo-HMM. The scores are reported in the
coordinate frame of a designated reference sequence (see
--refidx), which is by default the first sequence in the
alignment. They can be suppressed with the --no-post-probs
option. The secondary type of output, activated with the
--most-conserved (aka --viterbi) option, is a set of discrete
conserved elements. These elements are output in either BED or GFF
format, also in the coordinate system of the reference sequence
(see --most-conserved). They can be assigned log-odds scores
using the --score option.

[Pierre Lindenbaum]

but what is the difference of information between the wig and the txt.gz ?

[Ning-Yi Shao]

This problem I am not sure. The txt.gz files contain information about lod score in bed formation. I think those are the intermediate results of phastCon score program, for in case if somebody want to customize his own phastCon score. But I am not sure. Please check this webpage.

[Ning-Yi Shao]

This problem I am not sure. The txt.gz files contain information about lod score in bed formation (LOD=phastCons row log odds score). The further information you may check phastCon score program.

[Ning-Yi Shao]

This problem I am not sure. The txt.gz files contain information about lod score in bed formation (LOD=phastCons row log odds score). The further information you may check phastCon score program. It looks like the intermediate results of phastcon score program, and also can be used as measure of conservation. Please refer to this webpage.