Question: Questions About Column Output In Operate On Genomic Intervals -> Profile Annotations
0
James Wagner • 20 wrote:
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.
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modified 5.3 years ago
by
Jennifer Hillman Jackson ♦ 25k
•
written
5.3 years ago by
James Wagner • 20
