Chromosome Position In The Ucsc Phylop46Way.Placental.Wigfix File

Question

[Abdel]

Hi everyone
I downloaded the chr1.phyloP46way.placental.wigFix file from ucsc , i need it to get a phyloP score for a given position of the chr1 . My problem is that there is no position field in this file , just the scores...
0.056
0.056
0.056
0.064
0.056
0.064
0.056
. . .

Did someone know how am i supposed to figure out a chromosomic position ?

Answer 1

[Istvan Albert]

You have a fixed step wiggle file. Check the Wiggle specification:

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

[Abdel]

if i'm not mistaken , the phyloP score for the chr1 10918 is 0.064 it is intuitive , the confusing thing is that when querying ucsc table browser for this position ,i found a different value 0.0400079 (clade :mammal ,Group :comparative genomics ,track :conservation ,table :mammals Cons phyloP46wayPlacental) is that normal ?

Answer 2

[Pierre Lindenbaum]

Istvan is right and you missed the very first line of the wig file in your input: the wig starts at 10918 on chr1 and the distance between each value is 1. See the wig spec.

curl -s "ftp://biomirror.auckland.ac.nz/goldenpath/currentGenomes/Homo_sapiens/phyloP46way/placentalMammals/chr1.phyloP46way.placental.wigFix.gz" |\
gunzip -c |\
head

fixedStep chrom=chr1 start=10918 step=1
0.064
0.056
0.064
0.056
0.064
0.064
0.064
0.064
0.064

[Abdel]

if i'm not mistaken , the phyloP score for the chr1 10918 is 0.064 it is intuitive , the confusing thing is that when querying ucsc table browser for this position ,i found a different value 0.0400079 (clade :mammal ,Group :comparative genomics ,track :conservation ,table :mammals Cons phyloP46wayPlacental) is that normal ?

Answer 3

[Emma]

I have been having the same problem, i.e. I am getting different scores between the wigfix files (chr21.phastCons46way.placental.wigFix) and the galaxy platform (Placental Mammal Conservation by PhastCons), but for the phastCons score (hg19 in both databases):

fixedStep.chrom.chr21.start.9411194.step.1
                                     0.053
                                      0.044
                                      0.033
                                      0.017
                                      0.010
                                      0.008

and from galaxy:

variableStep chrom=chr21 span=1
9411194 0.0493701
9411195 0.0394961
9411196 0.029622
9411197 0.014811
9411198 0.00987402
9411199 0.00493701
9411200 0.00987402

I would be grateful if you mentioned how you solved your problem and what I could be missing.

[Istvan Albert]

Please don't post a new question in the answer section of an old question. Post a new standalone question if you have one that way you can get it answered.