Calculating phyloP conservation score over certain genomic region

phyloP scores can be used to identify the evolionary rate of genomic sequences. Positive score represents slower evolution or more conserved sequence and negative score represents faster evolution.

Pre-calculated phylop scores can be downloaded from UCSC site. The file is in bigwig format. Here, is step by step to calculate the phylop score for the given genomic region

• convert bigwig to bedGraph file

bigWigToBedGraph hg19.100way.phyloP100way.bw hg19.100way.phyloP100way.bedGraph

bigWigToBedGraph can be downloaded from here

• Use bedtools map to get mean score over the given genomic coordinates

bedtools map -a genomic_region.bed -b hg19.100way.phyloP100way.bedGraph -c 4 -o mean > phylop_score.bed

The parameter -c 4 means the phylop score is present in column 4 in the bedGraph file. You can also change the output to be based on other operators such as sum, count, median etc.

References

• paper
• tutorial
• phylop