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-   -   does tophat rescue PE reads that do not map by aligning a single end of the PE? (http://seqanswers.com/forums/showthread.php?t=13988)

zorph 09-09-2011 02:14 PM

does tophat rescue PE reads that do not map by aligning a single end of the PE?
 
I don't think it does as the Tophat manual states that it does not mix the single read and paired end reads together, hence how could it map single reads when starting out with PE. However this might be wrong. Does anyone know if this is true or not? Thanks.


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