Hi,
I have a basic question (+ 2 follow up questions) for which there seems to be no answer on the web or I'm applying the wrong search terms ...
1)
I am wondering about why the insert size in paired end (PE) experiments is constant?
I read everywhere that the typical read size or Illumina paired end reads is 2x75 or 2x100 or whatever, but nowhere seems to be explained why the insert size constant.
DNA is shreddered into pieces, so every fragment should be of random size or shouldn't it?
To me the answer must be that there is some sort of size filtering step (picking only fragments of size 300 for example, thus I throw away like 99% of the DNA? Because the percentage of fragments that have exactly size 300 should be low in the whole sample after the shreddering step). But I do not want to guess, I want to know. But IF there really is a size selection step, I wonder about 2 more things:
2.1) How is that done? I know that you could do it with a gel electrophoresis, but I thought the NGS machines would work whole-automatically so that there is no scientist who transfers samples onto a gel ...
2.2) Why would ancient DNA reads be shorter than the ones derived from non-ancient samples? I mean it's the same procedure right?
I have a basic question (+ 2 follow up questions) for which there seems to be no answer on the web or I'm applying the wrong search terms ...
1)
I am wondering about why the insert size in paired end (PE) experiments is constant?
I read everywhere that the typical read size or Illumina paired end reads is 2x75 or 2x100 or whatever, but nowhere seems to be explained why the insert size constant.
DNA is shreddered into pieces, so every fragment should be of random size or shouldn't it?
To me the answer must be that there is some sort of size filtering step (picking only fragments of size 300 for example, thus I throw away like 99% of the DNA? Because the percentage of fragments that have exactly size 300 should be low in the whole sample after the shreddering step). But I do not want to guess, I want to know. But IF there really is a size selection step, I wonder about 2 more things:
2.1) How is that done? I know that you could do it with a gel electrophoresis, but I thought the NGS machines would work whole-automatically so that there is no scientist who transfers samples onto a gel ...
2.2) Why would ancient DNA reads be shorter than the ones derived from non-ancient samples? I mean it's the same procedure right?
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