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Plotting Density Of Reads On Chromosomes

I want to plot a picture like this:

< image "20141014104516" not found >

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 .

rna-seq r next-gen genome
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updated by Ram Ram • written by scszsc • scszsc

Which one? :)

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updated by Ram Ram • written by Neilfws Neilfws

The picture has been updated

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updated by Ram Ram • written by scszsc • scszsc

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

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updated by Ram Ram • written by JC JC

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

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updated by Ram Ram • written by scszsc • scszsc

3 answers

  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)
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updated by Ram Ram • written by Renesh Renesh

What about a circos plot?

Circos Histogram Bam File

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updated by Ram Ram • written by Manu Prestat Manu Prestat

I wrote this tool some time ago: BamGenScan

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

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updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

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