[Galaxy-user] Problem in set-up of "coverage" operation
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.
T. Ming Chu Professor of Biochemistry and Molecular Biology