Question: unplaced, unlocalized, ... scaffolds from hg19 to GRCh38
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gravatar for tabone.olivier
3.9 years ago by
tabone.olivier0 wrote:

Dear all,

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 (ie : chr1, chr2, ..., chrY). It doesn't work for element coming from unplaced, unlocalized and alternative portions of chromosomes (for example chr6_cox_hap2, or GL000191.1, ...) 

So my question is: Is there a way to find correspondance between coordinates of alternative chromosomes from hg19 and the new ones on GRCh38 ?

Thank you,

Olivier

assembly • 1.8k views
ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by tabone.olivier0

as far as I know these elements do not exist anymore in hg38.

ADD REPLYlink written 3.9 years ago by Giovanni M Dall'Olio26k

Thank you for your answer. Ok they don't exist but i am still surprised there is no correspondance between unlocalized scaffolds (known chromosome, but unknown position within chromosome) from hg19 and the "good" position within chromosome in hg38.

 

ADD REPLYlink written 3.9 years ago by tabone.olivier0
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