Plotting large file size of bedtools genomecov output

Question

[nitinra]

Hi everyone,

I generated the output for coverage using bedrolls genomecov using this command:

bedtools genomecov -ibam input.sorted.bam > output.coverage -bga

The resulting files are huge (range of 5-6gb/file). I do not think it is possible for me to use R to plot the histogram since it is so huge. Is there a way to plot it using other tools on command line? Thank you for your help.

Here is my output:

Chromosome_1    0   24  0
Chromosome_1    24  52  2
Chromosome_1    52  82  3
Chromosome_1    118 202 2
Chromosome_1    202 268 1

Thank you!

Answer 1

[Pierre Lindenbaum]

use bedtools mergewith option -o and -c to aggregate/reduce the size of the bed file.

https://bedtools.readthedocs.io/en/latest/content/tools/merge.html