Can anyone tell me about the bet tools for alternative splicing detection and quantification?

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Rafik Neme

If you are working with model organisms for which there are reference genomes, you can try cufflinks (http://cole-trapnell-lab.github.io/cufflinks/tools/), or stringtie (https://ccb.jhu.edu/software/stringtie/), also referenced commonly as the tuxedo tools. Note that you will probably need a few of the other tuxedo tools, such as bowtie, etc. But those websites provide good guides for beginners.

Additionally, you can try this that showed up in my feed not too long ago. Seems worth exploring. http://sjcockell.me/2015/05/18/alignment-free-transcriptome-quantification/

Alicia Poplawski

I used DEXSeq and SplicingCompass for mouse data.