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Old 10-15-2014, 06:42 PM   #2
blancha
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Location: Montreal

Join Date: May 2013
Posts: 367
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We only do stranded RNA-Seq at our institute.

It eliminates the ambiguity when you have genes at the same location on opposite strands. This is often the case for non-coding RNA, and protein-coding genes. The results can be distorted if you assign the reads from a non-coding RNA to a protein-coding gene.

I only see advantages to stranded RNA-Seq which is why we do it systematically, regardless of the objective of the experiment.

I don't do the library prep myself, only the bioinformatics analysis. The molecular biology platform at our institute does the library prep using a dUTP protocol. Since they do it systematically, partly upon my recommendation, I can't imagine it adds much work to the library prep.
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