How To Plot The Coverage Of A Region In The Genome

Question

[hellbio]

HI,

I would like to plot the coverage distribution of the targeted region and the genome. For this i have used genomeCoverageBed and coverageBed functions from Bedtools and got the output from the two functions.

Could some one suggest a way or Rscript to plot 1. coverage distribution for target region (X-axis:depths=1,5,10... and Yaxis:fraction of target bases covered)

1. coverage for genome (X-axis:depths=1,5,10... and Yaxis:fraction of target bases covered)

from the Bedtools outptut?

[Pavel Senin]

how exactly your data (to be R input) looks like?

Answer 1

[Sean Davis]

See the GenomicRanges package for dealing with aligned reads and regions. In particular, you may find the coverage() function useful.

[hellbio]

But, working in R with huge datasets needs huge memory and time. So is there any alternate way?