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Old 03-16-2014, 07:05 PM   #15
rskr
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Location: Santa Fe, NM

Join Date: Oct 2010
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Quote:
Originally Posted by gringer View Post
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.
IMO it is obvious that Tophat went to transcriptome mapping because they were unable to solve the pseudo gene problem, what remains to be seen is does using the genome actually bring anything to the table besides huge hardware requirements, and short leading and trailing non-coding isoform? Could whatever it does bring to the table be done later with the reads that don't map to a transcript? In an analysis that is different than differential expression, like an isoform search...

Furthermore, I think most poorly characterized organisms get the transcriptomes done first since they are easier, and provide a majority of the useful information, which sort of renders the argument about uncharacterized organisms, mute.
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