Hello Jen and other members, here is a history with the interval dataset I
uploaded and the results I get when doing a Profile Annotations summary. In
particular I am concerned about why in some cases tableChromosomeCoverage <
tableRegionCoverage and allCoverage < nrCoverage.

https://main.g2.bx.psu.edu/u/jwag/h/unnamed-history

Thanks so much


On Thu, Aug 15, 2013 at 12:55 AM, Jennifer Jackson <j...@bx.psu.edu> wrote:

>  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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>
> --
> Jennifer Hillman-Jacksonhttp://galaxyproject.org
>
>
___________________________________________________________
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