Hello, I would like a clear and simple answer on the difference of splice aware / splice unaware aligners. There is a discussion that @dfernan generated but for me the definition is not very clear. Can you help me please. :D
Splice aware aligners like tophat, STAR provide bam out put with spliced junction information (specific locations where introns are removed) whereas non splice aware aligners like bowtie2 do not do this.