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Old 02-24-2014, 02:19 AM   #1
dalesan
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Location: portugal

Join Date: Feb 2011
Posts: 15
Question Differential Expression: is it better to map reads to genome or transcriptome?

Hello, hello.

This may be a very naive question, but I haven't been able to find an established answer yet in the literature, nor here (bad search technique, perhaps).

I'm about to embark upon a differential expression analysis (Arabidopsis) but before doing so, I wanted to know if any of you can comment on the potential benefits/drawbacks of using the transcriptome as a reference rather than the genome?

Presumably, by using the transcriptome, one circumvents having to deal with junction libraries and such. On the other hand, when using a transcriptome annotation, one will have to limit the mapping to the most representative transcript isoform so as to avoid multireads.

In your experience, if we choose to disregard splicing for the moment and focus only on DE, would you map your reads to the genome or the transcriptome, and why?

I'm thinking I might just do both and compare the results. But it would be nice to hear your thoughts.

Thanks!!
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