I'm working with whole-genome sequencing data and I already did the alignment and I have my bam files. I calculated the coverage per genome position of those bam files with bedtools:
bedtools genomecov -ibam file.bam -d > coverage.txt
My problem is that
coverage.txt is 50GB. I tried to visualize this with R in the cluster but it runs out of memory. So my doubts: do you know how could I reduce the size of this file? Maybe there is a better way to calculate and visualize genome coverage?
Any help would be appreciated!