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Old 09-25-2012, 07:43 PM   #2
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Location: The University of Melbourne, AUSTRALIA

Join Date: Apr 2008
Posts: 275

I think there are a few reasons people use PE for RNA-Seq:

1. Most sequencing centres only do PE 100bp so there is no choice

2. Illumina pricing PE doesn't cost that much more than SE (changing with MiSeq)

3. Many people want to do DGE, but may want to also denovo assemble, where PE is better

4. PE reads might be more uniquely alignable to the genome than a SE read. And for DGE, that is important. However PE does not give more statistical power than SE, as all that matters is counting tags, and a PE reads and a SE read both count as a single tag.

FYI - for bacteria, we try to use SE 50bp for RNA-Seq, as we don't have isoform/splice variant issues, and 50bp is enough to map uniquely.
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