To maximize splice junction identification, a spice junction search step was added prior to the final mapping (Figure 3) because TopHat mapping using externally supplied splice junction information can identify additional splice junctions (http://tophat.cbcb.umd.edu/manual.html). For this step, three gene specific libraries provided a large population of GABAB1 gene specific splice junctions. After mapping individual libraries, all splice junction data were collected and used for the final mapping of the alcoholic and control whole transcriptome libraries (Figure 3).
