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Old 01-22-2012, 07:17 AM   #1
ahli1981
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Default convert hg19 to hg18, chr mismatch

when I convert hg19 to hg18, some positions from chr3 in hg19 are matched to chr2 in hg18. e.g. chr2:5144329 in hg19 are matched to chr3:165545129
Does anyone know why?
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Old 01-22-2012, 09:33 AM   #2
Heisman
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Interesting; I have not seen that. It looks like portions of the chromosomes were rearranged between the different assemblies. If you download the liftOver hg19 to hg18 chain file and type in
Code:
grep 'chr 2' [hg19_to_hg18_chainfile] | grep 'chr 3' | less
you will see:

Code:
chain 25982 chr2 243199373 + 16340754 16341023 chr3 199501827 - 118072788 118073057 6523537
chain 4737 chr2 243199373 + 5145834 5145884 chr3 199501827 - 155139362 155139412 33407240
chain 4607 chr2 243199373 + 5145066 5145350 chr3 199501827 + 191348934 191349218 1967131
chain 2538 chr2 243199373 + 16338477 16338504 chr3 199501827 - 154040818 154040845 35425972
chain 1237 chr2 243199373 + 5143151 5144336 chr3 199501827 - 33955506 33956705 3724972
The position you listed would fall within the last line.
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Old 01-23-2012, 06:39 AM   #3
husamia
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have you tried to look at the sequence to see if its the same?
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