I'm referring to the Segmental Duplications track:
How do I interpret the arrows (I suppose that's the strand)? Does that mean that duplication only happens in a given strand? Where is exactly this segment inserted when duplicated? Are the breaking points anywhere within this region? or are breaking points at the start or end of the block?
I guess my general issue is that I don't know what they represent in a person with the duplication vs the reference genome. Could anyone make a visual example like a graph? (I know what duplications are I just don't know this specific notation UCSC is using).
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You're showing the "Segmental Duplications" track, not the Repeatmasker track.
The arrows are backwards if the other sequence, the one that aligns here, is on the negative strand. The arrows are forward if the other sequence is also on the forward strand (unless you clicked the "reverse" button before, which reverses the strand of the genome browser, then you'd need to inverse what I wrote)
True it's Segmental Duplications, I just edited the question. However I'm not sure what you mean. Why do the arrows matter for a duplication? The duplication is not a gene, it's not necesarily being sequenced so why not put all the duplications in the + strand.
The direction is kind of useful, you want to know if it's on the forward or the reverse strand. If the segment includes genes, it's good to know if they're on the reverse strand there or not. We have the information about the strand, so why would we not show it?
Maybe you have genes in that region being transcribed in both ways? The DNA duplication is observed always in both strands, not just one. It's just the duplication event that happens in one strand.
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It may depend on the tool, could you provide details on the duplication track? There cannot be insertions that exist only in one strand. Intuitively, I would assume that > (forward) means that the direction of the insert is the same as the other sequence(s), otherwise (<) that the insert sequence is on the opposite strand relative to the other sequence(s). If there are multiple sequences the direction depends on the selected reference.
I guess my question is why do we care about direction? It's a region not a gene. Why not put all the info on the positive strand. I unfortunately don't have anymore details, the documentation is a bit poor in my opinion: https://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=3914588883_6wAduqvy74ixYtg1AxhZ7PAtdcVj&db=hg19&c=chr10&g=genomicSuperDups
Can you provide more context to the screenshot above? You are referring to repeatmasker track but what you are showing is not that track correct? It looks like a "variation" track of some kind.
True since it was under "Repeats" I got confused. But it's the "Segmental Duplication" track.