Hi Yan,
Thank you for your question about the LiftOver tool in the UCSC
Genome Browser.
Based on a small experiment, it appears that the order of regions in
the input is maintained in the output as well. For example, I used
web-based LiftOver to convert the following regions from hg38 to
hg19:
chrX 151383000 151390000 region1
chrX 151183000 151190000 region2
chrX 151073054 151173000 region3
chrX 151283000 151290000 region4
chr1 100000000 100005000 region5
And the order of these regions was maintained in the output:
chrX 150551472 150558472 region1
chrX 150351472 150358472 region2
chrX 150241526 150341472 region3
chrX 150451472 150458472 region4
chr1 100465556 100470556 region5
This little experiment was limited in scope and may not reflect
what's done with a large amount on regions or with regions that map
to multiple locations. I would highly recommend that you give each
region a unique name in the input so that input regions can be
definitively matched with output regions.
Additionally, if your SNPs have rsIDs associated with them, you may
be able to use the snp147.txt.gz files we have on our downloads
server and some UNIX commands like "grep" to extract the regions for
these SNPs from the most recent SNP build available in the UCSC
Genome Browser. You can find the snp147.txt.gz here:
http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/snp147.txt.gz.
I hope this is helpful. If you have any further questions, please
reply to
gen...@soe.ucsc.edu. All messages sent to that address are
archived on a publicly-accessible Google Groups forum. If your
question includes sensitive data, you may send it instead to
genom...@soe.ucsc.edu.
Matthew Speir
UCSC Genome Bioinformatics Group