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Old 10-07-2013, 07:58 AM   #4
Location: oslo

Join Date: Jun 2012
Posts: 11
Default 50 bp single end sequencing

Hi Torst,

I see this reply of yours is rather old, but IŽd like to follow up on this: do you use 50 bp SE sequencing for bacterial RNA-seq?

I am doing some bacterial RNA-seq myself, ran a few samples on MiSeq 2x150. I will now do more samples on the HiSeq, but not really sure that 2x100 is worth the additional cost....



Originally Posted by Torst View Post
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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