Add '--norc' option to Bowtie for eXpress.

In the stranded reads case, to match the Bowtie command executed by RSEM.
Document '--rc' Bowtie option for eXpress.
Consistent naming for scatter plots.

i.e. include either 'gene' or 'transcript' in the name depending on the level
at which the graph is being plotted.
Remove interpreter directives from python modules.

i.e. from those that used to be executable, but are now called from a script in
the bin directory.
Randomly reassign read pair strands in unstranded case.

Fixes #51.
A little rationalisation of plot function params.