Question: Ideas From Using Galaxy2
gravatar for Belinda M. Giardine
12.9 years ago by
Belinda M. Giardine70 wrote:
While I was trying to do an example showing Galaxy2, I found myself looking for tools that weren't available. When working with the mutations it would be nice to have some function for getting exact matches, possibly even using the name field. When the data is mixed with very large and very small regions just overlap isn't always to most informative. Mutations also give you up to 3 names for a single nt region. It would take incorporating the name field to distinguish these. Also when it comes to looking at the queries there is nothing for displaying more than 1 at a time. It would be nice to be able to view them as multiple user tracks at UCSC. Also graphs that show more than 1 query? I would have liked somehow either graph or at least a number in a column to be able to get a count of the number of regions that overlapped each region in a second query. Similar to coverage but with counts. Belinda
galaxy • 861 views
ADD COMMENTlink modified 12.9 years ago by James Taylor320 • written 12.9 years ago by Belinda M. Giardine70
gravatar for James Taylor
12.9 years ago by
James Taylor320
United States
James Taylor320 wrote:
I'm not sure exactly what you mean. Join with the option of matching additional fields? Some kind of filter / match tool that would allow a variable number of input queries could be quite useful. Perhaps the easiest thing to do would be to make a script that does what you want, then integrate it into Galaxy. Yes, a "build UCSC custom track" tool would be awesome. All of these tools could be built using the multi-page "wizard" tool functionality that is in the framework but not used by many tools. Some modifications would be needed, but it should be straightforward. The idea would be that a tool could provide a "wizard controller" class that would evaluate the current tool state and return the appropriate configuration for the next page or a signal to dispatch to the tool runner. Most of the pieces are already in place. Yes, we've been talking about a tool for progressively building complicated plots for a while. Bob recently expressed some interest in working on this. This could also be a wizard, the fist page would have general plot configuration and from there you would have the option of wither "add another line [pointset, whatever]" or "execute/finish".
ADD COMMENTlink written 12.9 years ago by James Taylor320
Pretty much yes. The scenerio was that I had done overlap with mutations and some other query getting back the mutations. I had also done the same thing with a different second query. Then what I wondered was how many mutations were in both results. I couldn't use overlap since large deletions overlap many other mutations. Even if there was an overlap with exact match option that wouldn't give me the answer I was looking for if any of the mutations had the same coordinates (ie A>G, A>C, A>T each listed as a different mutation). Belinda
ADD REPLYlink written 12.9 years ago by Belinda M. Giardine70
Hi, Could you please include Eucalyptus genome ( in the public version of Galaxy. It is being sequenced at JGI and recently 8x assembly was completed. Thank you, Regards, Bala Thumma
ADD REPLYlink written 8.3 years ago by Reddy.Thumma@csiro.au10
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