How To Design Suitable Library For The Detection Of Alternative Splicing And Fusion Genes By Rna-Seq ?

Question

[jack]

Which library design (single end or paired end, short or long read length) would you choose for the detection of alternative splicing and fusion genes by RNA-Seq?

[Floris Brenk]

Generally the longer the reads the better and easier the mappability to the genome is and paired end data is always better than single end due to that the mate pair always improves the mapping and assembling the transcriptome as well.