Plot per base coverage from regions coverage with R
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Entering edit mode
2.5 years ago
jeni ▴ 60

Hi!

I have a dataframe with some oligonucleotides coverage inside genomic region: the first column indicates its genomic coordinates and the second indicates its coverage.

12:36761802-36761804 54

12:36761802-36761805 42

12:36761802-36761806 56.5

12:36761802-36761810 28.75

12:36761803-36761804 29

12:36761803-36761806 30

How could I generate a per-base coverage plot? As you can see, this regions are overlapping, so I would like to know how can I get a plot with genomic position in the x axis and coverage in the y axis.

Thanks

R • 517 views
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Entering edit mode
2.5 years ago

You can use karyoploteR to achieve something like this

enter image description here

Source: https://bernatgel.github.io/karyoploter_tutoria

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