When running some of the quantifiers (e.g. RSEM, Cufflinks), I'm specifying that the reads come from a stranded protocol. But in fact, this is only the case when paired-end reads are simulated - I should remove these options in the single-end case (but first check what affect that has on accuracy).
When running some of the quantifiers (e.g. RSEM, Cufflinks), I'm specifying that the reads come from a stranded protocol. But in fact, this is only the case when paired-end reads are simulated - I should remove these options in the single-end case (but first check what affect that has on accuracy).