Plotting Depth Of Reads On Chromosomes

[sc-zsc]

I want to plot a picture like the attachment picture. Short reads(21-30bp) mapped to genome with bowtie . And then, Plot the reads density and depth of each chomosome, with a sliding window(1 K).

Could you give me some advice ? Thanks.

[Brian Bushnell]

It's hard for me to make out that picture, but you can generate histograms of the coverage across chromosomes (per base or binned) from a sam file using pileup.sh, like this:

pileup.sh in=mapped.sam out=coverage.txt

It's available here; you can run it with no arguments to display help information. It does not generate an image, just a tab-delimited-column text file that you can plot in, for example, R or Excel.