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Questions tagged [liftover]

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2
votes
0answers
12 views

hgsql not found when running a script despite being accessible on command-line

I am working on macOS. I am following the steps described here to lift over an annotation from the reference genome of C. elegans to another assembly of C. elegans. I have run this code: ...
1
vote
1answer
38 views

Accessing UCSC genome via ssh results in a validation error

I am working on macOS High Sierra. I am following the steps described here to lift an annotation over from one version of a genome to another. I am now just using the example genomes provided in the ...
3
votes
0answers
14 views

dog coordinates (canFam3) to human coordinates (hg19)

I've converted dog coordinates to human using UCSC LiftOver. These are 200bp intergenic regions that are differentially methylated from normal dogs to cancer dogs. I've converted these to human ...
6
votes
2answers
296 views

How can I compare two bed files?

I am trying to translate (lift over) bed files describing genomic regions from hg37 to hg38. I have tried both UCSC's LiftOver tool and CrossMap but saw that they give me different results. I ...
8
votes
4answers
114 views

Working with old genome builds

Is working with and relying on old genome builds still valid? For example NCBI36/hg18. Would results from papers based on old builds require LiftOver and re-analysis to be useful? A bit of context, ...