We plan to do an RNA-Seq analysis of knockdown and control samples in order to analyse differences in alternative splicing patterns between the two groups. The analysis should be done using R package SGSeq. We would now like to know which parameters we have to choose for the RNA-Seq experiment that allow us to do the analysis with SGSeq lateron.
We know that we need strand-specific sequencing with long paired end reads (100bp-150bp). We are however unsure about the sequencing depth. Do you have suggestions for that?
Thank you for your help,