I've had a long break, and last time I learnt about it, I thought PE reads are required for detection and quantification of differential isoform expression. A few days ago someone was trying to convince me that long SE reads (100-150bp) can do as well. Any comments/ideas/opinions?
I am planning an RNA-seq experiment now, and need to decide if I want to pay 2x for PE, or can settle for SE. My main interest will be in DE of genes, but if I already do it, I'd rather have a dataset that'll allow me to look at isoform expression, TSS usage etc. too later on (if I recall correctly, CuffDiff could do all that).
Thanks in advance for good advice,