phastcon conservation score for chip seq peaks

Question

[varsha619]

Hi, I would like to do get conservation scores for my ChIP-seq peaks. Is phastcon the best method to use? I have read the following threads but am still not sure what is the best way to go about this -

Get Conservation Score Of Chromosome Region

How To Calculate Conservation Score Of Given Bed Regions

I would like to compare between various species of insects and vertebrates as well. Is there a way to do this directly using my ChIP peak bed files? Thank you.

[varsha619]

Does anyone know an equivalent of http://ceas.cbi.pku.edu.cn/submit.htm for species other than mice and human?

[varsha619]

I used these steps to get my phastcons scores -

1. Get the bw file from UCSC
2. Convert bigWigToBedGraph and bedGraph to bed (awk '{print $1 "\t" $2 "\t" $3 "\t" $4}')
3. bedtools intersect -a ChIP_peaks.bed -b phastCons.bed

Is this the best way to do this? My final goal is to plot a PhastCons score vs Distance from Binding site plot. Please advice.

Answer 1

[Alex Reynolds]

If I remember, phastcon data gives conservation scores over regions, while phyloP offers conservation scoring on a per-base basis. Depends on your experiment which is better or more appropriate. Here is a method I detail for calculating phyloP scores for regions of interest (peaks, motif binding sites, whatever):

A: Conservation score for a piece of human genome

[varsha619]

Thanks @Alex Reynolds, I was wondering if there is any existing program available for what your in-house perl script does?

[Alex Reynolds]

Not sure, maybe others would know!