So, I am trying to use STAR aligner to do some splice junction analysis. My goal is to recapitulate the analysis published by DeBoever, et al., PLOS Computational Biology (2015). In their paper they used a splice junction database to call aberrant splicing events. I have what I thought was the correct splice junction file in the proper format to perform these alignments, but when I opened my SJ.out.tab documents today I found that almost all of my read counts where in the multi-mapping column rather than uniquely mapping column. I was wondering if anyone else has performed this type of analysis? Is is common when using a splice junction database in addition to the GTF file for reads to map multiple times or am I using the wrong database file? Any help would be greatly appreciated!