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Old 09-25-2013, 07:47 AM   #5
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Location: Auburn, AL

Join Date: May 2012
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Originally Posted by NicoBxl View Post
I don't think it's a good idea. It's always better to map to all the transcript because your data is coming from total RNA ( or poly-A RNA). It can happen that when you map to your subset, some reads maybe map in a better way to transcript that are not in your subset..
Yes, you're right. It is more robust to use entire assembly, since the result would be normalized by the entire mRNA expression, and also much easier for downstream analysis.
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