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Old 10-18-2013, 07:54 AM   #8
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Originally Posted by dpryan View Post
Sort of, though I can read that in ways that wouldn't be correct, so I'll clarify. If we C->T convert the reads (just read1 for paired-end data) and then align it to a bisulfite converted genome, the reads will be from a directional library if they only map forward on a C->T converted reference and reverse a G->A converted reference. If they also align appreciably in the reverse orientation on the C->T reference or forward on the G->A converted reference, then they very likely arose from a non-directional library prep. I could see someone misinterpreting what you wrote in the case of paired-end reads.

Since bisulfite treatment results in a loss of proper base-pairing between DNA strands, the new complementary oligos that are created in some library preps are then sometimes referred to as being complementary. Yeah, I can see where the confusion arises there!
Ah, I see. Thanks for the clarification.

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