Hello Rathi, At this time, the best we can offer is the mm5 --> mm8 --> mm9 conversion method.
I understand your concern about the possible loss of data in doing multiple liftOvers. I've checked this out for you, and it turns out that lifting 2-3 times vs lifting directly has been pretty much identical with mouse and human genomes. You can see if any of the originals are lost and if so go from there. But anything that makes it through will be accurate. The thing about the mouse assemblies is that they're all still the same genome. They're 99.9% identical.(Lifting mm9 -> hg18 -> rn5 would be a disaster though.) I hope this information is helpful to you. Please don't hesitate to contact us again if you require further assistance. Kayla Smith UCSC Genome Bioinformatics Group ----- "Rathi Thiagarajan" <[email protected]> wrote: > Hi there, > > I am currently trying to identify the transcription start sites (TSS) > of a > number of genes based on the information from CAGE sequencing tag > provided > in the Riken CAGE DB (http://gerg01.gsc.riken.jp/cage/)for mouse. > > Unfortunately, the coordinates available for the CAGE tags are only > available for the mm5 (May 2004)version of the mouse genome. I see > that > UCSC Genome Browser conversions for mm5 are only available up to mm8. > Is > it possible to obtain, the mm5-mm9 conversions? My concerns about > doing a > double conversion i.e mm5-mm8-mm9 would result in some loss of > resolution, > so I was wondering if there was any other way to go about this > please? > > Thanking you in advance. > > Cheers, > Rathi > > -- > Rathi Thiagarajan > Expression Genomics Laboratory / Grimmond Laboratory > Institute for Molecular Bioscience > University of Queensland, St. Lucia, QLD 4072 > AUSTRALIA > Tel +61 7 3346 2609 > Fax +61 7 3346 2101 > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
