Question: Same liftover position for different positions
0
gravatar for priyanka16161
3.0 years ago by
priyanka161610 wrote:

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

liftover genome • 845 views
ADD COMMENTlink modified 3.0 years ago by dyollluap300 • written 3.0 years ago by priyanka161610
3
gravatar for Devon Ryan
3.0 years ago by
Devon Ryan93k
Freiburg, Germany
Devon Ryan93k wrote:

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 COMMENTlink written 3.0 years ago by Devon Ryan93k
0
gravatar for dyollluap
3.0 years ago by
dyollluap300
USA, California, Bay Area
dyollluap300 wrote:

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

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

ADD COMMENTlink written 3.0 years ago by dyollluap300
1

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

ADD REPLYlink written 3.0 years ago by Devon Ryan93k

What's the difference between both tools?

ADD REPLYlink written 3.0 years ago by ddiez1.8k
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