I transformed genome coordinates from hg19 to coordinates of GRCh38 using the function
liftover() from rtracklayer package in R. I used the
hg19ToHg38.over.chain file from UCSC. But it only contains chromosome from primary assembly (i.e., chr1, chr2, ..., chrY). It doesn't work for element coming from unplaced, unlocalized and alternative portions of chromosomes (for example
So my question is: Is there a way to find correspondence between coordinates of alternative chromosomes from hg19 and the new ones on GRCh38?