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Date: 2025-07-10 01:02:42
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Though the illumina graphic shared above is used widely, it is infact misleading.

You can consult these videos to see what is going on inside of a sequencer.

https://www.youtube.com/watch?v=fCd6B5HRaZ8&list=TLPQMTAwNzIwMjUtLuqPiOfGHw&index=1

https://www.youtube.com/watch?v=HMyCqWhwB8E&list=TLPQMTAwNzIwMjUtLuqPiOfGHw&index=2

If you watch carefully, Read 1 (R1) is sequenced from the forward strand of the DNA template, whereas Read 2 (R2) is sequenced from the reverse strand of the same DNA template.

So while R1 and R2 are not exactly the reverse complement of each other (although they can be in instances like dovetailing or when one mate contains the other), they are read from the opposite ends of complementary DNA sequences.

So in a case where R1 would map to the forward strand of the genome, its mate R2 would map to the reverse strand (or the reverse complement of R2 would map to the forward strand of the genome).

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Posted by: Shruti Singh Kakan