Lift-over between genome versions

[emdann]

Description of feature

Feature description: easily converting genomic coordinates of annotations between genome assemblies (or easy access to download gene model for different assembly)

In Bioconductor this is implemented in the liftOver function in rtracklayer, which works with GRanges objects and chain files from UCSC

library(rtracklayer)
path = system.file(package="liftOver", "extdata", "hg38ToHg19.over.chain")
ch = import.chain(path)
seqlevelsStyle(gr_obj) = "UCSC"  # necessary
cur19 = liftOver(gr_obj, ch)

Possible solutions

• Specify Ensembl release with genome assembly of interest (to check: is there a specific release for a genome assembly? I don't think so)
• Interact with Open2C people

[ivirshup]

We'll consider this out of scope for now