Don't unzip reads before mapping

This hasn't been required in tophat for a long time, and slows us down.
Don't call cufflinks in MapReads

Mapping is different from abundance estimation.  Since we may want to use
different reads than the ones we just mapped (e.g. the rescued reads), it may
even be a waste of our time.
Add rescue_reads to do_research
Make base genome data files and bowtie-builds

Gotta make sure to do EVERYTHING we need.
Sort rescued files as well
First attempt at a pared-down cufflinks/cuffdiff script

At the moment, only doing the cuffdiff call.  That means we're not getting the
individual values for each of the samples, but for all the analyses, I'm using
the combined data only anyways.