make an average conservation plot based on ChIP-seq data

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How to make an average conservation plot from ChIP-seq data Hi all, I want to know how to make an average conservation plot http://ceas.cbi.pku.edu.cn/ this website can make something I want, but it can only plot a set of regions at one time, I want to plot two sets of regions, and compare them. " 2. GC content and evolutionary conservation of each ChIP-region and their average. CEAS uses PhastCons conservation scores from UCSC Genome Bioinformatics, which is based on multiz alignment of human, chimp, mouse, rat, dog, chicken, fugu, and zebrafish genomic DNA. CEAS generates thumbnail conservation plot for each ChIP-region and the average conservation plot for all the ChIP-regions, which can be directly used in ChIP-chip biologists' manuscript. " Any python scripts or bioconductor package can do it? Thanks

04-22-2013, 02:05 AM	#2
paolo.kunder Member Location: Milano, Italy Join Date: Aug 2011 Posts: 56	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