Hi Dubravka,
Thank you for your question about converting a region from mm6 to
mm10. The reason you are encountering that error is because the
region you are trying to convert may be too large. Large regions do
not lift as well because there is an increased chance that these
will span a region that has changed between the two assemblies. When
you run into an issue like this, you may want to consider splitting
the region you are trying to convert into a few smaller regions.
Here are some basic steps that you can use to determine whether or
not a large region is comparable between two assemblies:
- Take some sequence from the beginning and end of your region
in the original assembly, in this case mm6.
- Separately BLAT these two sequences against the target
assembly, which would be mm10 in this case.
- If these sequences exist in the new assembly, you can find the
ends of the region in the new assembly.
- Compare the size of the region between the assemblies to see
if it is a reasonable region to compare between the two
assemblies.
Since mm6 is not available on the web-based LiftOver tool, you can
use the available mm6 to mm10 LiftOver file and the command line
liftOver utility to convert between the two assemblies. You can find
the command line liftOver utility here:
http://hgdownload.soe.ucsc.edu/admin/exe/. You can run the liftOver
utility on the command line without any arguments to see the usage
message and options. You can then find the mm6 to mm10 LiftOver file
here:
http://hgdownload.soe.ucsc.edu/goldenPath/mm6/liftOver/.
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