I want to plot a picture like this:
Short reads mapped to genome with bowtie etc. And then, Plot the reads density and depth of each chomosome, with a sliding window(1 K).
Could you give me some advice ? Thanks .
check R:Bioconductor packages 'GRanges' and 'ggbio'.
I will check the two packages. Thanks for your help.
Which one? :)
The picture has been updated
What about a circos plot?
Circos Histogram Bam File
I wrote this tool some times ago: BamGenScan https://github.com/lindenb/jvarkit/wiki/BamGenScan
but didn't use it much (= use cautiously)