Hi,
I am just trying to liftover the following genomic region from hg18 to hg19.
chr6 29677984 33485635
When I used liftOver() in rtracklayer, I obtained the following results.
> hla.gr.hg18 <- GRanges(seqnames="chr6",IRanges(29677984,33485635))
> chain <- import.chain("./hg18ToHg19.over.chain")
> hla.gr.hg19 <- liftOver(hla.gr.hg18,chain)
> hla.gr.hg19
GRangesList of length 1:
$1
GRanges with 8 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr6 [29570005, 31963859] *
[2] chr6 [31963877, 31964315] *
[3] chr6 [31964332, 31964390] *
[4] chr6 [31964396, 31996597] *
[5] chr6 [31996615, 31997053] *
[6] chr6 [31997070, 31997128] *
[7] chr6 [31997133, 32012535] *
[8] chr6 [32012537, 33377657] *
When I used the binary for liftover from UCSC as follows,
./liftOver input.bed hg18ToHg19.over.chain output.bed unlifted.bed
output.bed contained only one interval: chr6 29570005 33377657
Can anyone explain to me the reason for this difference in liftover?
I am just trying to liftover the following genomic region from hg18 to hg19.
chr6 29677984 33485635
When I used liftOver() in rtracklayer, I obtained the following results.
> hla.gr.hg18 <- GRanges(seqnames="chr6",IRanges(29677984,33485635))
> chain <- import.chain("./hg18ToHg19.over.chain")
> hla.gr.hg19 <- liftOver(hla.gr.hg18,chain)
> hla.gr.hg19
GRangesList of length 1:
$1
GRanges with 8 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr6 [29570005, 31963859] *
[2] chr6 [31963877, 31964315] *
[3] chr6 [31964332, 31964390] *
[4] chr6 [31964396, 31996597] *
[5] chr6 [31996615, 31997053] *
[6] chr6 [31997070, 31997128] *
[7] chr6 [31997133, 32012535] *
[8] chr6 [32012537, 33377657] *
When I used the binary for liftover from UCSC as follows,
./liftOver input.bed hg18ToHg19.over.chain output.bed unlifted.bed
output.bed contained only one interval: chr6 29570005 33377657
Can anyone explain to me the reason for this difference in liftover?
