Hi Heisman,
I Just need a simple clarification please.
Suppose you have a read like (AAACGGCGTTTCCC)
and you want to sequence it using Illumina paired end runs.
Does paired end mean you will get the sequence of the ends?
i.e does it imply we only sequence AAA and CCC in the sequence above.
if it is true, I assumed that using sequencing by synthesis we would get TTT and GGG.
I understand that if we mapped the sequences back to the reference we would anticipate that they are 8 bases apart (given no INDELS are present in our DNA at hand). Is this right?
However, I am majorly concerned about the sequence in between.
What really happens to it?
I guess my question is:
What is the benefit of paired end reads if we only sequence the ends and not whats in between?
I would really appreciate the help on clarifying this thought
I Just need a simple clarification please.
Suppose you have a read like (AAACGGCGTTTCCC)
and you want to sequence it using Illumina paired end runs.
Does paired end mean you will get the sequence of the ends?
i.e does it imply we only sequence AAA and CCC in the sequence above.
if it is true, I assumed that using sequencing by synthesis we would get TTT and GGG.
I understand that if we mapped the sequences back to the reference we would anticipate that they are 8 bases apart (given no INDELS are present in our DNA at hand). Is this right?
However, I am majorly concerned about the sequence in between.
What really happens to it?
I guess my question is:
What is the benefit of paired end reads if we only sequence the ends and not whats in between?
I would really appreciate the help on clarifying this thought
Originally posted by Heisman
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