Hello Tom,
Your regions (like QTL regions in general) are very large, so there is
almost
never a chain that maps the entire region to a different species. QTLs are
very
fuzzy by nature ("a trait seems to be transmitted with this part of the
chromosome") and lifting them across species just adds more uncertainty: the
mystery gene (or regulatory element?!) *might* be in one of the many resulting
regions in the other species, or not.
Despite the inherent sketchiness of liftOvering such large fuzzy things as
QTLs, we tried to do a coarse mapping of mouse and rat QTLs to human. If you
really want to try it with your regions, please refer to this file in the
source
code: kent/src/hg/makeDb/doc/hg18.txt, section "# RGD RAT QTL MAPPED TO
HUMAN",
and skip down to the "#====== end discarded work."
You can obtain the source tree either via CVS:
http://genome.ucsc.edu/admin/cvs.html
or a zip file:
http://hgdownload.cse.ucsc.edu/admin/jksrc.zip
I hope this information is helpful to you. Please don't hesitate to contact
the mail list again if you require further assistance.
Regards,
----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
Moloshok, Thomas [CNTUS Non-J&J] wrote:
> Good morning,
>
> I have successfully used your LiftOver utility in the past, but today
> all 8 of my queries are failing with the message "deleted in new"
>
> I am trying to map the rat QTL regions:
>
> Chr4:69183301-134858710
>
> Chr12:1-29130348
>
> Chr10:35713452-101848683
>
> Chr7:90478161-135478161
>
> Chr3:139485124-171063335
>
> Chr2:210636008-247306073
>
> Chr10:35713561-36254741
>
> Chr10:69160380-86317054
>
> To the human genome.
>
> I don't know of any other means to do this.
>
> BLAT might work if I could go cross species with the chromosomal
> location (these pieces are large enough that this would be the method of
> choice).
>
> The tables that you provide might also be possible, but I don't see that
> any provide what I am really looking for.
>
>
>
> Do you have any suggestions?
>
>
>
> Thanks,
>
> Tom
>
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
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