Updated script to use full Trinity assembly including contaminant reads. Confirmed previous Sailfish mapping results.
After evaluating the effect of removing contaminants prior to quantifying gene expresssion,
determined best course of action was to quantify expression for all genes and then remove
the contaminants. This strategy ensures that reads associated with contaminants are removed
during the quantification step.

Updated script to follow this quantification strategy. In process, updated to use Sailfish v0.6.3
which required some updates to the "sailfish quant" step.