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.