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Old 11-28-2011, 05:52 AM   #4
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Location: Purdue University, West Lafayette, Indiana

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The vast majority of RNAseq protocols use fragmented RNA or cDNA for library construction. This is because there are limits on the length of PCR products that can be generated in a PCR reaction. Or rather, I should write, short PCR products are more robustly amplified than long ones.

Also, even if you see that polyA tail, you are still inferring that is the transcribed strand. Whereas you can use strand-specific methods to assay which strand it is. Get it? One is a presumption you are making (whether for good reason or not), the other is an observation.

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