Added TOPHAT_OPTIONS Environmental variable to tophatcuff.sh.
Added TOPHAT_OPTIONS Environmental variable to tophatcuff.sh.

To specify options for tophat in the config file.

Version to test with LNCaP/PrEC Directional Seq

clark-lab/ngsane,aehrc/ngsane,clark-lab/ngsane,aehrc/ngsane,aehrc/ngsane,BauerLab/ngsane,BauerLab/ngsane,clark-lab/ngsane,aehrc/ngsane,BauerLab/ngsane,clark-lab/ngsane,BauerLab/ngsane