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Old 06-16-2014, 12:37 AM   #4
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
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The strand-specificity relates to the strand from which whatever you're sequencing arose. That is, if you're looking at reads that cover an mRNA on the + strand, then read #1 from those will all (or almost all) be on one the + strand. If, however, you're looking at reads covering an mRNA on the - strand, then read #1 will (normally) be on the - strand. It wouldn't be very useful to have a kit that always gave reads on the + strand.

N.B. some kits reverse things, such that read #1 will be on the - strand if the mRNA is on the + strand. I think those are mostly for SOLiD sequencing, so you're unlikely to bump into them anymore.
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