Quote:
Originally Posted by NicoBxl
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..
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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.