converting hg11 genomic coordinates to hg19

[Prithvi Raj]

Hello UCSC team,

Thanks for helping the community with genomic database.

I need some help with conversion of hg11 coordinates to hg19. The liftover functionality on UCSC browser does not list hg11 build.

Thanks for your help and suggestions!
Prithvi

UT Southwestern Medical Center

Dallas

 

 

---

UT Southwestern

Medical Center

The future of medicine, today.

[Christopher Lee]

Hi Prithvi,

Thank you for your question about converting coordinates between hg11
and hg19. We have created the liftOver chains needed to perform the
coordinate conversion, they are available for download here:
http://hgdownload.soe.ucsc.edu/goldenPath/hg11/liftOver/

Once you have the hg11ToHg19.over.chain.gz file downloaded, you can
run the command line version of liftOver to convert your hg11
coordinates to hg19 like so:
liftOver hg11.coordinates hg11ToHg19.over.chain.gz newCoords.bed
unMappedCoords.bed

You can obtain liftOver from the genome-store here:
https://genome-store.ucsc.edu/

liftOver is free for personal and non-profit academic research use.
For more information on running liftOver, run the program with no
arguments to read the usage message.

Please let us know if you have any further questions!

Christopher Lee
UCSC Genomics Institute

Want to share the Browser with colleagues?
Host a workshop: http://bit.ly/ucscTraining

Thank you again for your inquiry and using the UCSC Genome Browser. 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 forum. If your question includes sensitive data,
you may send it instead to genom...@soe.ucsc.edu.

> --
>
> ---
> You received this message because you are subscribed to the Google Groups
> "UCSC Genome Browser Public Support" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to genome+un...@soe.ucsc.edu.
> To post to this group, send email to gen...@soe.ucsc.edu.
> Visit this group at https://groups.google.com/a/soe.ucsc.edu/group/genome/.
> To view this discussion on the web visit
> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/C6B5A4A5-B10C-43FF-BC70-10135B19703F%40utsouthwestern.edu.
> For more options, visit https://groups.google.com/a/soe.ucsc.edu/d/optout.