Are all bs-seq strand-specific? How can I tell if a library is not strand-specific? If we say the proportion or the methylation level of a gene , does it only refer to the methylation on the positive strand?
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Cacau
Almost all BSseq libraries produced these days are strand-specific. To double check this, just use a million or so reads and see how they align to all 4 strands of a non-directional reference (you can do this with Bismark or Bison or most other BSseq aligners). If you get low percentage alignments to the complementary strands then you have a strand-specific dataset.
Methylation of a gene refers to both strands.
In my opinion, single-end BS-sequencing should be non-directional library while paired-end BS-sequencing should be directional library. How do you think about it @Devon?
Either one can be directional or not, it's dependent on how the library is made. The SE/PE nature of the actual sequencing doesn't end up affecting this.
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