Question: LiftOver with zero-based UCSC chain file
0
gravatar for Zhenyu Zhang
3.0 years ago by
Zhenyu Zhang240
United States
Zhenyu Zhang240 wrote:

I am planing to do some LiftOver from hg19 to 38. Well there is the tool and UCSC chain file. However, I roughly remember that UCSC uses zero-based coordinates, which is different from others. Will this create a problem? Should I edit ucsc chain file first by adding 1? 

chain file liftover ucsc • 943 views
ADD COMMENTlink modified 3.0 years ago by Devon Ryan88k • written 3.0 years ago by Zhenyu Zhang240
0
gravatar for Devon Ryan
3.0 years ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

A given format always uses the same coordinate system. This will work perfectly fine as long as the chromosome names are compatible.

ADD COMMENTlink written 3.0 years ago by Devon Ryan88k

So what you mean is that the effect of 0 vs 1 will cancel out, and I shouldn't be worried about it. Is that right? 

ADD REPLYlink written 3.0 years ago by Zhenyu Zhang240

No, what I mean is that there is no difference between UCSC and anything else. A format is a format, regardless of where it's from.

Edit: Perhaps I should mention that the tool itself has 0-based coordinates in mind.

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by Devon Ryan88k
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