Hello, I tried using this tool today after
inputting a bed file containing 1509 intervals of 100 bp each,
spread across all 22 autosomes.
First of all, despite the fact that my input file contained
intervals for 22 chromosomes, the value of "allCoverage"
seemed to be the same as the value of the coverage of that
table only for chr1. I was not really sure about the
tableRegionCoverage column, as for most of the autosomes I had
input data spread throughout the chromsome with points a few
Mb away from either end, but I was getting a value in this
column only about 1/3 of what I get when downloading the data
directly from UCSC and summing the interval sizes.
There were also many cases where nrCoverage >
allCoverage, even when I reduced each input genomic interval
to only 1 bp to avoid redundancy in the input file. Based on
these descriptions of the columns I would expect allCoverage
>= nrCoverage at all times.
Just wondering if you could clarify what these columns are
supposed to mean or how to reconcile these apparent
inconsistencies.