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Old 03-16-2014, 05:26 PM   #14
gringer
David Eccles (gringer)
 
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 838
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I would recommend mapping to the genome, but using the transcriptome as a mapping template to pick up splice boundaries, etc.. In other words, something like what Tophat does. Mapping to the genome makes novel isoforms a bit easier to pick up, and mapping to the transcriptome will give you more descriptive output (e.g. proper gene names) with a bit less work. I would expect that thaliana should have a fairly well-annotated transcriptome, so you'll be losing a lot by ignoring annotated genetic features.
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