Encode best practices, how many clusters?

[Matt.Ralston]

Hello, SeqAnswers. I'm sure someone has a quick fix here. The Encode best practices guide suggests 30M paired end reads for simple D.E. and 100M+ paired end for isoform/transcript discovery. http://encodeproject.org/ENCODE/prot...dards_V1.0.pdf
Is 30M paired end reads synonymous with 15M sequenced clusters or 30M sequenced cluster (60M reads)?
Thank you!

[dpryan]

I would interpret that to mean 30 million pairs, so 30 million clusters. Having said that, it seems a bit high given some recent papers (though those likely preceded the recommendations), not to mention that paired-end are often overkill for simple DE analysis, at least of well annotated organisms.