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My professor in class said the following statements.

  1. Short reads can map break points
  2. Long reads can disambiguate repeat related issues

I'm very new to genomics, so I don't quite understand the first statement. What is meant by short reads can map break points. What are break points to begin with?

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    $\begingroup$ Did you ask your prof.? He/she is quite likely to answer your questions. $\endgroup$ – Devon Ryan Apr 15 at 7:26
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    $\begingroup$ The professor's explanations are not quite clear to me and only confuse me more. Hence, I figured I ask here. $\endgroup$ – Jonathan Apr 15 at 15:56
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Short reads can map break points

With short reads you do an "indirect observation/inference" of a structural variant: based on your paired-end reads you figure out something is wrong because their distance or orientation is not what you expect. With long reads, you often get a direct observation of a breakpoint, with sufficient long reads on both sides (either split alignment or spanning the SV) allowing almost nucleotide accuracy.

Long reads can disambiguate repeat related issues

Short reads cannot align unambiguously in many repetitive regions, because the repeat is longer than the read. Long reads, however, span most common repeats entirely, allowing you to unambiguously assign a location for each read, as such resolving the issues.

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  • $\begingroup$ I'd say "paired short reads can approximately locate breakpoints", because short single end reads will not do a good job, since they can't detect a breakpoints unless they land right on top of it. Paired end reads will tell you approximately where a large structural variation is, but won't give you base resolution, unless the read happens to sit right on the breakpoint. $\endgroup$ – swbarnes2 Apr 18 at 17:03
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A "break point" typically denotes one end of a structural variation, such as an inversion or deletion. You can simply think of it as the position where the normal chromosome was broken to allow the variation. One can find these with short (Illumina) reads relatively easily since with paired end sequencing you'll have pairs spanning these breakpoints with odd relative orientations or insert sizes or such. Note that this is not a particular strength of short reads, since long reads are probably even better at this (they are not as good for finding SNPs at the moment though).

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