Question

Same liftover position for different positions

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7.2 years ago

priyanka16161 • 0

HI while doing liftover from GRCh36 to GRCh37 using UCSC Genome Browser, I got same liftover position for different positions of GRCh36. For example: chr6:4636693-4636693 to 4691694-4691694 chr6:74606747-74606747 to 4691694-4691694 Is it possible to get liftover positions like this?

Thanks

genome liftover • 1.6k views

ADD COMMENT • link updated 7.2 years ago by dyollluap ▴ 310 • written 7.2 years ago by priyanka16161 • 0

score 3 · Answer 1 · 2017-01-30

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7.2 years ago

Devon Ryan 104k

This is certainly possible, there were a number of assembly problems in the earlier releases. I realize that this can create...difficulties in interpreting whatever you're lifting over. If you can, perhaps go straight to GRCh38 instead, which has fewer issues than GRCh37.

ADD COMMENT • link 7.2 years ago by Devon Ryan 104k

score 0 · Answer 2 · 2017-01-30

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7.2 years ago

dyollluap ▴ 310

You could try it with the NCBI remap tool instead of the UCSC liftOver.

https://www.ncbi.nlm.nih.gov/genome/tools/remap

ADD COMMENT • link 7.2 years ago by dyollluap ▴ 310

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This sort of behavior will be observed regardless of the tool.

ADD REPLY • link 7.2 years ago by Devon Ryan 104k

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What's the difference between both tools?

ADD REPLY • link 7.2 years ago by ddiez ★ 2.0k