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Old 10-18-2013, 07:51 AM   #6
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

Originally Posted by pmiguel View Post
"Complementary strands"? Do you mean the following?:

For a bisulfite-converted library, you would look some of the reads and see if all the conversions are C->T or G->A. If so, it is a stranded library. If the reads are mixed (about 1/2 have all C->T and the other 1/2 have all G->A conversions), then the library is not stranded.
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!
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