Create mean coverage plot

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7.1 years ago

Bella_p ▴ 70

Hi :) I'm a newbie in bioinformatics and R programming, so I'll appreciate any help. I have few excel files with mean coverage at different locations of different genes at different chromosomes (each excel file contains the same genes locations, only the mean coverage changes). I'm trying to plot the data as one of the following plots:

PLOT

Anyone know the plot and know to tell me how to do it?

Thanks!

sequencing NGS COVERAGE R • 1.9k views

ADD COMMENT • link 7.1 years ago by Bella_p ▴ 70

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Where is your example plot?

You might be interested to check deepTools (which I'm using a lot these days), ngs.plot to avoid dealing with a number of excel files (i.e. you can directly process bam files).

ADD REPLY • link 7.1 years ago by venu 7.1k

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![Mean coverage[1]

ADD REPLY • link 7.1 years ago by Bella_p ▴ 70

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I fixed the link for the plot in the original post.

ADD REPLY • link 7.1 years ago by GenoMax 147k

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You may want to take a look at my recent posting here: C: Histogram showing overlap between 2 bed files

It looks like an ordered version of my my plot, i.e., they've ordered the coverage from low-to-high, and added horizontal bars for things like upper- and lower- quartiles (I presume)

ADD REPLY • link 7.1 years ago by Kevin Blighe 88k

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