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Old 04-22-2013, 02:05 AM   #2
paolo.kunder
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Location: Milano, Italy

Join Date: Aug 2011
Posts: 93
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Hi,

I encountered the same problem few weeks ago,

It seems that there are not many "expert" regarding PhastCons in this forum.

I explain you what I did,

I took my Chip-seq regions, in bed file format, intersect them with PhastCons element in (mouse example)

Code:
http://hgdownload-test.cse.ucsc.edu/goldenPath/mm9/phastCons30way/

and calculated for each genomic position the score of conservation.
Then averaged all the score.

Consider that you will need to transform a bit the PhastCons file format,

for example:

original format ( just replaced some words with empty)
Code:
chrom=chr1 start=3000306
0.006
0.010
0.014
chrom=chrX start=40000306
0.014
chrom=chr9 start=80000306 
0.1
0.2
processed format
Code:
chr1 3000306 3000307 0.006
chr1 3000307 3000308 0.010
chr1 3000308 3000309 0.019
chrX 40000306 40000307 0.014
chr9 80000306 80000307 0.1
chr9 80000307 80000308 0.2
with the following script:
Code:
awk '/^chrom/{split($1,a,"=");split($2,b,"=");next} { printf "%s\t%10d\t%10d\t%f\n",a[2],b[2],b[2]+1,$1;b[2]++}' filename


Another possibility that I am investigating is using circos
HTML Code:
http://circos.ca/
but You will need to study first how the software works,

Cheers,
Paolo
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