I need to draw the shape of peaks from different chip-seq samples.
I want to get something like this picture, which I found on a Nature paper.
Can you help me in doing that?
Thanks
I need to draw the shape of peaks from different chip-seq samples.
I want to get something like this picture, which I found on a Nature paper.
Can you help me in doing that?
Thanks
I've never done this before, but I think you could do something like the following:
1. Get the summit position of all the peaks in your sample and convert them to BED format.
2. Expand the summit position upstream and downstream by 2,500 bp (like in the figure), using bedtools slop.
e.g. bedtools slop -i summits.bed -g my.genome -b 2500 > summits.2500.bed
3. Calculate the per base pair coverage for each peak region using bedtools coverage.
e.g. bedtools coverage -counts -d -a summits.2500.bed -b sample.bam
4. Load the coverage data in R, modify it so that you take the average coverage for each position, then plot a scatter plot of position against coverage.
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I also a fan of deepTools for this. They also have a Galaxy server for those that want to avoid the command-line. Disclaimer: I have never used their Galaxy server.