[Galaxy-user] Fwd: Problem in set-up of "coverage" operation

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[Galaxy-user] Fwd: Problem in set-up of "coverage" operation

Ross Hardison
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: [hidden email] (Yi Zhang)
Date: April 17, 2006 10:34:22 AM EDT
To: Ross Hardison <[hidden email]>
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
phone: 814-863-0113              FAX: 814-863-7024






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Galaxy-user mailing list



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





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Re: Fwd: Problem in set-up of "coverage" operation

Yi Zhang
Now it has been fixed on all the versions of galaxy.

Thanks for Istvan's help.

Yi

On Wed, Apr 19, 2006 at 10:28:31AM -0400, Ross Hardison wrote:

> 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: [hidden email] (Yi Zhang)
> >Date: April 17, 2006 10:34:22 AM EDT
> >To: Ross Hardison <[hidden email]>
> >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: [hidden email]
> >>phone: 814-863-0113              FAX: 814-863-7024
> >>
> >>
> >>
> >>
> >>
> >
> >>_______________________________________________
> >>Galaxy-user mailing list
> >>[hidden email]
> >>http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
> >
> >
>
> Ross Hardison
> T. Ming Chu Professor of Biochemistry and Molecular Biology
> The Pennsylvania State University
> 304 Wartik Laboratory
> University Park, PA 16802
> e-mail: [hidden email]
> phone: 814-863-0113              FAX: 814-863-7024
>
>
>
>
>