To maximize splice junction mining from whole transcriptome libraries, a splice junction search step was implemented prior to final mapping. At this step we collected splice junctions from the .bed files of the individual mapping results from all gene specific and whole transcriptome libraries. After the combined .bed files were converted uniquely to a .juncs file, the alcoholic and control whole transcriptome library data were remapped using the .juncs file with -j option of TopHat. After recollecting splice junction data from the mapping, we generated a new .juncs file that contained additional splice junction information and visualized it using the UCSC genome browser.
