tsv file genome coverage
Hello, I have a tsv file that looks like this :
I want to know what is the file's coverage of the genome. The data in it represents cut sites of crisper cas9 in T cells.
I tried to follow this post, but it always gives the same answer for any input in tsv format. command:
bc <<< "scale=10; 100 * $(awk '{sum=$3-$2}END{print sum}' /groups/itay_mayrose/kimk/targets_file_Leenay_mean_eff_coordinates.tsv) / $(awk '{sum+=$2}END{print sum}' hg38.chrom.sizes)"
output:.0000006231
I also know there are 1556 sites of length 20 in the file if it helps.
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kimkes25 •
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Could it be chromosome identifier? Your file has bare numbers and UCSC files typically have
chrprefix. See if it works if you add achrprefix to your chromosome identifiers.