non-strand-specific library for bs-seq

Question

[Cacau]

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?

Answer 1

[Devon Ryan]

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.