I have questions regarding sequencing:
Are paired-end reads from different stands? What about single reads, are they coming from both strands?
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Mates in a pair are giving signal for a single strand, though this is only apparent in bisulfite-treated samples. The reason for this is that you are sequencing the ends of fragments of material and it's random which strand of this (or both in different clusters) will get sequenced. Different pairs of reads will then randomly sequence one strand or the other.
Single-end reads are the same as paired-end reads, the second read in the pair is just not made.