R package for easy mm9 <-> mm10 / hg19 <-> hg38
devtools::install_github("caleblareau/easyLift")
Grab the convenient Rscript from the vignettes
folder
to run everything from the command line like so--
lareauc$ Rscript easyLiftOver.R randPeaks.bed hg19_hg38
[1] "Attempted to write to file: randPeaks.bedover"
.bed
file that one wants to lift over..bed
file supplied in the first argument. For the second (map
) parameter, we currently support any one of:
- mm9_mm10
- mm10_mm9
- hg19_hg38
- hg38_hg19
For the first (from
) parameter, the file extension doesn't necessarily need to be .bed
but just resemble a .bed
(e.g. .narrowPeak
In the R
environment, using easyLift::easyLiftOver
on a GRanges
object will return a GRanges
object with lifted over coordinates again specified by the second (map
) parameter.
If you have a .chain
file that you want to use (e.g. for going from mm10 to hg38), specify that file path in the second argument. This gives a sample URL structure to access these cross-species chain files from UCSC.
http://hgdownload.cse.ucsc.edu/goldenpath/hg38/vsMm10/
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