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,
best regards,
Andrea
Dear Leonhard,
one more question occured while discussing about the project. Is there a requirement for the length of the fragments generated in the library preparation? You also said that longer reads would be helpful. We would plan to do 2x150bp (40 mio reads per sample). Would you say that should work?
Best,
Andrea
There is no specific requirement for fragment or read length. I would follow standard recommendations for library preparation. The sequencing specs and read length sound fine.