Hi, I'm using UCSC liftover to convert hg19 to hg38, and I have a question because the result came out that I don't understand.
(I didn't check "Allow multiple output regions".)
I think the value of chr1:120904787 and chr1:149400430 should be the same value, not different.
Also, I checked the browser, and I think the mapping does not appear to be correct. (chr1:120904787(hg19) → chr1:143905854(hg38))
The result was the same even if I downloaded the chain file (hg19ToHg38.over.chain.gz) and used the PyLiftover.
If you know the reason, please reply.
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Mailtrack 21. 07. 16. 오후 03:36:13
Our liftOver chains are taken from the nets, and the nets are single-coverage on the target genome (currently the "from" genome, although there are cases in which it might make sense to go the other way).
When a region of hg19 maps well to two different regions of hg38, only one of those regions is kept in the net & liftOver chains, and conversely, when a region of hg38 maps well to two different regions of hg19, only one can be kept. So we expect there to be some regions that don't map symmetrically because the single-coverage restriction means they can't.
UCSC Cell Browser, Quality Assurance and Data Wrangler
Human Cell Atlas, User Experience Researcher
UCSC Genome Browser, User Support
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