UCSC liftover


Hi, I'm using UCSC liftover to convert hg19 to hg38.

The result came out that I don't understand.

Feb. 2009 (GRCh37/hg19) → Dec. 2013 (GRCh38/hg38) - chr1:120904787 → chr1:143905854

Dec. 2013 (GRCh38/hg38) → Feb. 2009 (GRCh37/hg19) - chr1:143905854 → chr1:149400430

(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.

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.






The original mapping does not appear to be correct. This is the original GRCh37 region; you can see FAM72B to the left, FCGR1B to the right, with NOTCH2 further left and SRGAP2C further right. The region UCSC have mapped it to contains genes that appear to be paralogues, FAM72C and SRGAP2D.

The second mapping, back to GRCh37, seems to be correct, as this region on GRCh37 contains FAM72C.

The correct mapping of your original locus should be to 1:121118498 which has NOTCH and FCGR1B to the left and FAM72B and SRGAP2C to the right.

Both regions are quite difficult as they both contain gaps in GRCh37 which have been filled in GRCh38 with some reorganisation (ie the two genes FAM72B and FCGR1B have flipped over). They also appear to be paralogous regions with similar genes in them.

before adding your answer.

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