Hello Vaibhav,

To compare the new and prior annotation (the genome is unchanged, making liftOver unnecessary), the best tool to use would be "Operate on Genomic Intervals" -> "Profile Annotations". Select the option for "Genes and Gene Prediction Tracks" as a starting place. The comparison data will be from UCSC's existing gene tracks from rn4.

Thanks for using Galaxy!

Galaxy team

On 12/29/10 1:41 PM, vaibhav jain wrote:
Hi all,
I have data with RGSC 3.4 build, along with the start and end
coordinates of genes. I want to use lift-over tool to get the
corresponding coordinates of those genes for Rat Nov. 2004 (Baylor
3.4/rn4) Assembly.
So how I can do this using lift-over ???
Or is there any other method to do this work ???

Thanks in advance

Vaibhav Jain
Research Scholar

Jennifer Jackson
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