Calculating human genome covering each segment
Hi
I have some genomic ranges like
Chr start end
1 10583 863511
1 12841835 12854479
I want to know for instance;
The range of 10583 to 863511 on chromosome 1 does cover how much of the genome
People say
tab$range_fraction <- (tab$end - tab$start) / human_genome_size
I am wondering what I should put as human_genome_size
Googling turns that human genome is 3,234.83 Mbp (mega-basepairs) per haploid genome and 6,469.66 Mbp total (diploid). Should I use haploid or diploid genome size as dominator?
Although I am not certain about what google shows
1 answer
Genome sizes always refer to the haploid genome. Get the chromSizes files from RefSeq or similar sources to get the sizes of all chromsomes. https://hgdownload-test.gi.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes
From there it is just (interval size) / (total genome), sure you can implement that.
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Hello A!
It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/13019/the-percentage-of-genome-with-copy-number
This is typically not recommended as it runs the risk of annoying people in both communities.