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Old 03-14-2014, 09:27 AM   #7
Location: Istanbul, Turkey

Join Date: Oct 2012
Posts: 28

Originally Posted by dalesan View Post
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.

I would appreciate if you can share your results, because I also wonder how much it differs when mapped on genome or transcriptome.
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