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Old 03-16-2014, 12:19 PM   #13
Location: portugal

Join Date: Feb 2011
Posts: 15

Originally Posted by Brian Bushnell View Post
Also, mapping to a genome is more objective and repeatable. Mapping to a transcriptome is very subjective, as there are a huge number of ways to design one. Add a single gene, or a single transcript, and the mappings of all reads may be affected. So, how do you choose which transcripts and isoforms to include? All of them? Just the longest for each gene? Just a full concatenation of all exons per gene? Just the ones that were known prior to date XYZ, or also the two new ones your lab found that you think are relevant? You'll get different results based on this purely subjective decision, possibly allowing results to be tweaked as desired.
Excellent points, Brian. I didn't think of it this way, in terms of the repeatability aspect. In my analysis I've limited the mapping to simply the longest isoform in the annotation. Neverthless, I'm curious to see how the results compare when I get back to my desk tomorrow.
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