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Old 11-22-2011, 01:34 PM   #4
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Location: San Diego

Join Date: May 2008
Posts: 912

I would agree with Soleil...the way people use forward and reverse in NGS context, the forward read is the one that is in the same direction as your reference, and the reverse is the one that is in the opposite direction. Of course, what might be forward for a genone might be reverse when talking about a transcript.

If you were doing something other than an ordinary genomic prep, like you were doing PCR, with the adaptors incorporated into the PCR primers, and putting that product onto the flow cell, then there would be a solid correlation between read 1 and the direction of the read itsself, with respect to the reference. But with ordinary genomic-type preps, the DNA gets sheared, and adaptors are ligated, and they don't know which way the DNA was oriented with respect to the telomere, or whether your reference puts the telomere at the start or the end of your refeence. So reads go in all directions. So really, all that matters is that for each cluster, read 1 runs one way, and read 2 runs the other way; towards each other in paired end, away from each other in mate-pair.
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