tsv file genome coverage

Question

[kimkes25]

Hello, I have a tsv file that looks like this :

picture sharing

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.

[vkkodali_ncbi]

Could it be chromosome identifier? Your file has bare numbers and UCSC files typically have chr prefix. See if it works if you add a chr prefix to your chromosome identifiers.