Bedtools coverage histogram
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4 months ago
User000 ▴ 490

Hello,

I am following this tutorial in order to plot che coverage depth for my target exomes: Visualize coverage for targeted NGS (exome) experiments. I also want to produce a plot similar to the post.

So I am using the following command line for all my bam files:

bedtools coverage -hist -abam {} -b input.bed | grep ^all > {}.hist.all.txt

I get an output where depth of coverage is either 0 or 1. But in the plot from the post the values are from 0 to 400. If i change bam files as -b and bed file as -a the output is empty. Why is that and what am I doing wrong?

all     0       697333613       802606707       0.5315176
all     1       105273094       802606707       0.4684824
bedtools • 324 views
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Entering edit mode

Could you show us the plot ? How to add an image on Biostars.

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