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Old 02-24-2014, 02:40 PM   #5
Location: portugal

Join Date: Feb 2011
Posts: 15

Thanks guys for the replies. I appreciate your input. At this point, I think I'm going to run a test comparison between using the genome vs transcriptome to see how congruent the results are when it comes to simple DE testing.

As Bukowski mentioned, mapping to the genome offers you much more information, including discovery of novel transcripts and isoforms. I do have another phase of my project that will consider alternative splicing and I'll definitely be mapping to the genome for this.
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