How To Calculate Conservation Score Of Given Bed Regions

Question

[User 6762]

Is there any simple way of extracting 44way or 29 mammals conservation levels of given genomic regions in human genome (BED format) ?

Answer 1

[Pierre Lindenbaum]

44way conservation levels are available as a set of WIG/BIGWIG files at the UCSC. For example, see: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/phastCons46way/primates/

you can query and convert those wig/bigwig files using wigtobigwig and bigWigToBedGraph in http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/

================================================================
========   bigWigToBedGraph   ====================================
================================================================
bigWigToBedGraph - Convert from bigWig to bedGraph format.
usage:
   bigWigToBedGraph in.bigWig out.bedGraph
options:
   -chrom=chr1 - if set restrict output to given chromosome
   -start=N - if set, restrict output to only that over start
   -end=N - if set, restict output to only that under end
   -udcDir=/dir/to/cache - place to put cache for remote bigBed/bigWigs

[Tafelplankje]

29 mammals is not there. you can find it here, already in bed format. http://www.broadinstitute.org/scientific-community/science/projects/mammals-models/29-mammals-project-supplementary-info

extraction of regions can be done with bedtools i think?

[Pierre Lindenbaum]

i removed "29 mammals"

[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.

P.S: I am working with an insect genome, most of the available tools seem to be for human genomes.

Answer 2

[Pascal]

In the title you ask how to calculate the conservation score, and in the description just how to extract conservation score from multiple regions.

For extracting you might want to take a look at biopieces. It includes a program for exactly that purpose: http://code.google.com/p/biopieces/wiki/get_genome_phastcons

Of course, the genome and conservation scores have to be downloaded from UCSC and set up for biopieces first.

Answer 3

[User 6762]

I found an easy way, using CompleteMOTIFS tool. It gives average PhastCons scores of a given BED region. http://cmotifs.tchlab.org/cgi/pipeline_v3.cgi