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