I'm interested in using a sequence capture method and I was asked about the length of the inserts. I'm wondering what that means.
Is it the length of the fragments after shearing? Is it what is going to be read by the sequencer?
From my understanding, it's just the size of the fragments that you are going to sequence. Is that correct?
It depends. Often (as in Illumina) "short insert" or "fragment library" means a normal library where the DNA is sheared and the fragments are sequenced from both ends, while "long insert" or "LMP" or "mate-pair" will use different preparation in which the DNA is circularized or spliced in some way so that the molecule being sequenced is not an original genomic fragment. The orientation often differs from a fragment library and it will often need some preprocessing prior to use, removing linkers or so forth that are gluing together the chimeric fragments.
For PacBio, the difference between short and long insert is just the target length of the size-selected sheared fragments.
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So generally, it's just the sequence that is going to be read by a sequencer... it's a fragment of genomic DNA obtained by various methods (such as shearing), and that is keep to be analyzed (such as size selection, biotinylation, etc.).
Yes, in any case you end up with a DNA fragment that will be read by the sequencer in the same manner - the only difference is in library prep.