Optimize splice junction discovery (TopHat2)

[hanhel]

I've got human RNAseq data (Illumina HiSeq, 100 bp reads, paired ends) and one of the primary aims is to map alternative splicing patterns in specific tissues.

I've run Tophat2, with default settings (-r 100, hg19 refseq), and do detect tentative alternative splicing, however not at many variants as we might expect for certain genes.


Do you have any suggestions or recommendations on Tophat options or alternative software for optimizing discovery of splice junctions?


Thanks!