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Old 12-22-2010, 11:28 PM   #1
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Location: moscow

Join Date: Oct 2008
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Default tophat junction strand

Hi everybody,
does anybody know how tophat identifies strand of junctins?
i thought that tophat used donor and acceptor site sequences for it, but when i check it i find that all possible dinucleotides could be on corresponding positions (even NN, that is quite strange), certainly the most of junctions use canonical (GT-AG) sites in stated strand, but i found small but sufficient amount of junction that have GT-AG in direct strand but reverse strand is stated (or opposite). the only explanation that i can give for it is that tophat uses read sequences instead of reference to judge strand (i didn't check it). is it true?
manual climes that tophat uses only "GT-AG", "GC-AG" and "AT-AC", but it looks to be incorrect.
thanks in advance
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