Hi Mali,
Unfortunately there no simple tool like liftOver to do this. However you
can accomplish this by using some utilities from the kent source:
1. Create a BED file containing the coordinates you want to translate.
(http://genome.ucsc.edu/FAQ/FAQformat.html#format1)
2. Use the bedToPsl tool to convert your BED file to PSL format.
3. Then use pslMap tool with the all_mrna psl from that assembly to map
your coordinates to the PSLs.
(you can find the all_mrna psl file (e.g., all_mrna.txt.gz) by
clicking on the Annotation Database link for the desired assembly on our
downloads page: http://hgdownload.cse.ucsc.edu/downloads.html)
You can download these utilities (incl in the Kent Source) here:
http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads
Install Instructions: http://genome.ucsc.edu/admin/jk-install.html
Please let us know if you have any additional questions: [email protected]
-
Greg Roe
UCSC Genome Bioinformatics Group
On 9/12/11 1:59 AM, mali salmon wrote:
> Hello
> Is there an option in UCSC to convert genomic coordinates to cDNA
> coordinates? similar to LiftOver but between genomes and spliced
> transcripts.
> Thanks
> Mali
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> https://lists.soe.ucsc.edu/mailman/listinfo/genome
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