I was doing conservation analysis for some regions of interest and wanted to map PhyloP score onto the selected regions (in a .bed file). I got different results using different method.
For example, for chr10: 91853138-91853143
If I just use UCSC Table Browser, I will get phyloP as described here:
track type=wiggle_0 name="100 Vert. Cons" description="100 vertebrates Basewise Conservation by PhyloP"
91853138: -0.62474; 91853139: -0.0926929; 91853140: 0.27974; 91853141: -0.145898; 91853142: 0.332945; 91853143:* 0.758583*.
If I use the method described here, I would get
chr10 91853138 91853139 000048-000000|-0.051000
chr10 91853139 91853140 000048-000001|0.332000
chr10 91853140 91853141 000048-000002|-0.107000
chr10 91853141 91853142 000048-000003|0.357000
Notice that the second method only gives me the scores for 4 bases and they are different from the values acquired from the Table Browser.
I also tried the BigWigAverageOverBed utilities and it produced the same results as the second method. Could anyone explain why there's discrepancy? Did I overlook anything?
Thank you so much!