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Old 10-18-2013, 08:29 AM   #3
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Originally Posted by dpryan View Post
The Lister/Ecker 2009 dataset is directional. When in doubt, just align the first 100,000 or so reads as non-directional and then look at the alignment statistics. If it's not actually non-directional, then the complementary strands will have very few reads aligned to them.
"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.

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