I have done a liftover on a hg38 bed file to a hg19 bed file on Crossmap(Link) and found out that multiple queries were changed from chromosome 22 to chromosome 14. Should I just filter this or did I do something wrong?
Thank you very much.
Data: hg38
chr22 15690509 15690536 POTEH 28.8238274624 -
chr22 15698714 15698741 POTEH 69.8367597081 -
chr22 15698718 15698745 POTEH 63.510218446 +
chr22 15698719 15698746 POTEH 64.7710373827 +
chr22 15698720 15698747 POTEH 71.7040268333 -
chr22 15698720 15698747 POTEH 64.4982928966 +
hg19
chr14 19553737 19553764 POTEH 28.8238274624 -
chr14 19562046 19562073 POTEH 69.8367597081 -
chr14 19562052 19562079 POTEH 71.7040268333 -
Some of these were already filtered based on 27bp length. All of the data are 27bp. Chain file is this: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHg19.over.chain.gz
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skim •
1 answer
You didn't do anything wrong, if you zgrep chr22 hg38ToHg19.over.chain.gz | grep chr14 you'll see there's a bunch of sequence originally in chr14 that was moved to chr22. If you go over to the gencode website and scroll through the GRCh37 assembly issues, you'll see a LOT of them were fixed with the GRCh38 release.
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