Question: Plotting Density Of Reads On Chromosomes
1
gravatar for scszsc
6.0 years ago by
scszsc10
Australia
scszsc10 wrote:

I want to plot a picture like this:

20141014104516

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 next-gen R genome • 5.5k views
ADD COMMENTlink modified 6.0 years ago by Manu Prestat4.0k • written 6.0 years ago by scszsc10
1

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

ADD REPLYlink modified 6.0 years ago • written 6.0 years ago by JC11k

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

ADD REPLYlink written 6.0 years ago by scszsc10

Which one? :)

ADD REPLYlink written 6.0 years ago by Neilfws48k

The picture has been updated

ADD REPLYlink written 6.0 years ago by scszsc10
2
gravatar for Renesh
6.0 years ago by
Renesh1.9k
United States
Renesh1.9k wrote:
  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)
ADD COMMENTlink written 6.0 years ago by Renesh1.9k
2
gravatar for Manu Prestat
6.0 years ago by
Manu Prestat4.0k
Lyon, France
Manu Prestat4.0k wrote:

What about a circos plot?

Circos Histogram Bam File

 

ADD COMMENTlink written 6.0 years ago by Manu Prestat4.0k
1
gravatar for Pierre Lindenbaum
6.0 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum130k wrote:

I wrote this tool some times ago: BamGenScan https://github.com/lindenb/jvarkit/wiki/BamGenScan

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

 

ADD COMMENTlink written 6.0 years ago by Pierre Lindenbaum130k
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