I just noticed that this is fixed on Galaxy2.2-test, but it is not fixed on Galaxy2.1ENCODE. My understanding is that we are directing people to use Galaxy2.1ENCODE, so it is imperative that it be fixed on the recommended version. Of course, it seems like it should be fixed on all versions that have this tool.

- Ross

Begin forwarded message:

From: yizhang@bx.psu.edu (Yi Zhang) Date: April 17, 2006 10:34:22 AM EDT To: Ross Hardison rch8@psu.edu Subject: Re: [Galaxy-user] Problem in set-up of "coverage" operation

Fixed. Thanks for letting us know the problem.

Yi

On Sat, Apr 15, 2006 at 10:45:11AM -0400, Ross Hardison wrote:

...

The "coverage" tool is a great addition to the set, but I think the description is backwards from the execution.

The user selects: The density of elements of Query: (call it query 1) within Query: (call it query 2)

The explanation says: "Return entire regions from query 1 that overlap query2, and append two more fields at the end of the returned region: (1) the number of nucleotides for each returned region from query 1 that overlap a region from query 2 and (2) the percentage of the overlap for each region of query1: ..."

What you get is actually the opposite of the explanation. You get the regions from the 2nd query that contain regions from query 1, etc. The selection tools have query 2 as the target for finding elements from query 1, but the explanation treats query 1 as the target.

I think the first choice should be query 1 and the second choice be query 2. You could change the explanation, but I think it would be better to change the selection display. In that case, you would have something like:

Within Query: (pull down menu of choices for the target) Find the density of elements of Query: (pull down menu of choices for elements to find in the target).

Then the explanation will fit.

Ross Hardison T. Ming Chu Professor of Biochemistry and Molecular Biology The Pennsylvania State University 304 Wartik Laboratory University Park, PA 16802 e-mail: rch8@psu.edu phone: 814-863-0113 FAX: 814-863-7024

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Ross Hardison T. Ming Chu Professor of Biochemistry and Molecular Biology The Pennsylvania State University 304 Wartik Laboratory University Park, PA 16802 e-mail: rch8@psu.edu phone: 814-863-0113 FAX: 814-863-7024