Hi James,

Full column descriptions are at the bottom of the Profile Annotations tool form.

Are you working on the public Main Galaxy instance, or can you duplicate this on Main https://main.g2.bx.psu.edu/ (usegalaxy.org)? It would be helpful if you could share a history link and point to the dataset(s) with these values - at first pass they do seem off, but we can look into why. Leave all inputs and outputs undeleted in the history when you email back the share link please. You send email me directly to keep your data private.

How to share a history:
http://wiki.galaxyproject.org/Support#Shared_and_Published_data

Thanks!

Jen
Galaxy team

On 8/14/13 8:13 PM, James Wagner 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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