Plotting Density Of Reads On Chromosomes

Question

[scszsc]

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 .

[JC]

check R:Bioconductor packages 'GRanges' and 'ggbio'.

[scszsc]

I will check the two packages. Thanks for your help.

[Neilfws]

Which one? :)

[scszsc]

The picture has been updated

Answer 1

[Renesh]

1. Get the bam files after mapping to genome.
2. Sort bam files according to genome position.
3. Predefine window size (say 1Mbp).
4. Calculate number of reads within that window size
5. Standardize that count to get gene density
6. Plot these data (x= genome position (Mbp) and y=gene density)

Answer 2

[Manu Prestat]

What about a circos plot?

Circos Histogram Bam File

Answer 3

[Pierre Lindenbaum]

I wrote this tool some time ago: BamGenScan

but didn't use it much (= use cautiously)