Say if I have an ancestral strain, as well as 20 replicates. The 20 replicates are divided into 4 treatment groups, so 5 replicates per treatment group.
I have 4 .bam files for each treatment group containing 5 replicates per .bam file.
I also have the variant files.
How do I calculate the average coverage of the genome?
I'm confused on what file to use to calculate the average.
Do I use one of my treatment .bam files, a variant file, or the ancestral strain?
I have bedtools installed as well as genomecov, but I'm not sure how to obtain the average coverage value that I am looking for.
I have 4 .bam files for each treatment group containing 5 replicates per .bam file.
I also have the variant files.
How do I calculate the average coverage of the genome?
I'm confused on what file to use to calculate the average.
Do I use one of my treatment .bam files, a variant file, or the ancestral strain?
I have bedtools installed as well as genomecov, but I'm not sure how to obtain the average coverage value that I am looking for.
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