We grow old when we stop playing.
This booklet covers the brief history related to biochemistry; what data and information you could get out of CLIP-seq; how to analyze those data. In particular how computer science and mathematics contribute to robust data analysis, including hidden Markov model, random forest, SVM, etc.
Hopefully this book would build a bridge between biologists and geeky computational scientists, at least in RNA-protein interaction research fields. After reading this book, bio-readers would have clearer concept about how the raw data produced by your efforts would be literally cooked as findings with scientific meanings. On the other hand computational scientists would not only learn to appreciate the underlying biological mysteries but also make the link between figuring out computational algorithms and solving biological problems more tight.
PALMapper, the fusion of the short read mapper GenomeMapper and the short read aligner QPALMA, is an easy-to-use and flexible tool to accurately and efficiently align both transcriptome reads (spliced and unspliced) from RNA-Seq experiments against a reference genome.
PALMapper can be used on the command line or through a Web service, which is a customized version of the Galaxy framework.