Question: Convert hg19 coordinates to hg38 coordinates
0
gravatar for Chat-ra
26 days ago by
Chat-ra20
Chat-ra20 wrote:

Hello everyone!

I would like to convert hg19 coordinates to hg38 coordinates. The problem is that I don’t really have much informations in order to do so.

For example: The gene KLHL7 in hg19 the start is 23 145 353 and the end is 23 217 533. In hg38 the start is 23 105 758 and the end is 23 177 916. I’ve succeeded to convert the start and the end of a gene. Now I want to convert the position 23 195 610 of the gene KLHL7 in hg19 to hg38. But I don’t really know how to do that with that much information.

Can someone help me please ? Thank you for any suggestions!!!

assembly • 110 views
ADD COMMENTlink modified 26 days ago by Pierre Lindenbaum120k • written 26 days ago by Chat-ra20
3
gravatar for Pierre Lindenbaum
26 days ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum120k wrote:

ucsc liftover : https://genome.ucsc.edu/cgi-bin/hgLiftOver

ADD COMMENTlink written 26 days ago by Pierre Lindenbaum120k

I don't think that i've explain correctly my problem.

I've only one coordinate (in this example : 23 195 610) that is in the middle on the gene. I can't seem to use Liftover with only one coordinate

ADD REPLYlink written 26 days ago by Chat-ra20

just do chr?: 23195610-23195610

ADD REPLYlink written 26 days ago by alvarocentron9110
1
liftover : chr7:23195610-23195611

>  Successfully converted 1 record: View Conversions 

chr7:23155991-23155992
ADD REPLYlink written 26 days ago by Pierre Lindenbaum120k
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