[Genome] Errors in basewise primate conservation scores (phyloP) of 43 vertebrate genomes with Human (hg18)

[Richard Burhans]

Folks,

While using wigToBigWig to convert the primate phyloP scores for the 44-way 
alignment with hg18 to bigwig, I found several positions with multiple scores.  
Here are links to the files I was trying to convert:

        
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/phyloP44way/primates/chr1.phyloP44way.primate.wigFix.gz
        
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/phyloP44way/primates/chr2.phyloP44way.primate.wigFix.gz
        
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/phyloP44way/primates/chr3.phyloP44way.primate.wigFix.gz
        
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/phyloP44way/primates/chr4.phyloP44way.primate.wigFix.gz
        
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/phyloP44way/primates/chr13.phyloP44way.primate.wigFix.gz
        
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/phyloP44way/primates/chr16.phyloP44way.primate.wigFix.gz
        
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/phyloP44way/primates/chrY.phyloP44way.primate.wigFix.gz

Here's the problems I found along with proposed solutions:

        o chr1
                o more than one value for chr1 base 220000001
                o suggest changing line 195836790 to "fixedStep chrom=chr1 
start=220000002 step=1"

        o chr2
                o more than one value for chr2 base 60000001
                o more than one value for chr2 base 230000001
                o suggest changing line 59341383 to "fixedStep chrom=chr2 
start=60000002 step=1"
                o suggest changing line 222927573 to "fixedStep chrom=chr2 
start=230000002 step=1"

        o chr3
                o more than one value for chr3 base 180000001
                o suggest changing line 173437707 to "fixedStep chrom=chr3 
start=180000002 step=1"

        o chr4
                o more than one value for chr4 base 110000001
                o suggest changing line 104807632 to "fixedStep chrom=chr4 
start=110000002 step=1"

        o chr13
                o more than one value for chr13 base 60000001
                o suggest changing line 41706166 to "fixedStep chrom=chr13 
start=60000002 step=1"

        o chr16
                o more than one value for chr16 base 20000001
                o suggest changing line 19816949 to "fixedStep chrom=chr16 
start=20000002 step=1"

        o chrY
                o more than one value for chrY base 20000001
                o suggest changing line 16192938 to "fixedStep chrom=chrY 
start=20000002 step=1"

-rico
        






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