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Welcome to the SplicePL wiki!

SplicePL is a tool I developed to detect splice junctions from paired-end RNA-seq reads. It uses BLAT to align the reads to the reference genome, followed by a simple filtering of the spliced reads.

Why BLAT? Well, it found more known junctions than other tools I tried. I believe in benchmarking tools on the real data. I tried
TopHat (1.0.13), SpliceMap (3.3), and GSNAP. To my surprise, BLAT and simple filtering performs really well on my 130nt RNA-seq data.

In summary, if you have reads longer than 100 nt, you should give SplicePL a try.