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Old 03-26-2013, 01:54 PM   #1
griffon42
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Location: New York

Join Date: Jan 2009
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Default Tophat and/or Cufflinks: strict splice donor/acceptor requirements?

Hello all --

I have a question regarding Tophat's handling of sequence data at splice donor/acceptor junctions:

When calling a splice junction/splitting a read across an intron, does Tophat require a traditional splice donor (i.e. GU at 5' end of intron) and traditional splice acceptor (i.e. AG at 3' end of intron) sequence in order to make the junction call? In other words, would Tophat still be able to map reads split across gaps generated by other forms of RNA processing that do not obey traditional splice donor/acceptor sequence rules?

By extension, I have the same question for Cufflinks' rules in generating transcript models.

I wasn't able to find documentation of these sorts of behavior in either manual or elsewhere.

Thanks very much for the help!
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cufflinks, rna-seq, splicing, tophat

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