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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.

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  • $\begingroup$ Now, I understood from you that the mates in paired-end reads are coming from two different strands, but based on the figure in biostars.org/p/95803 and also some other sources, I implied that they are coming from two different stands as they are read from two different directions. Could you please help me in understanding this? $\endgroup$
    – Negin
    Commented Mar 26, 2020 at 15:08

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