Thanks, if anyone else is interested I found an updated repeatmasker file for mm9 at RepeatMasker's main site http://repeatmasker.org/PreMaskedGenomes.html -Ed
On Tue, Sep 21, 2010 at 12:41 PM, Brooke Rhead <[email protected]> wrote: > Hi Ed, > > We don't have any plans to update the RepeatMasker track on mm9. One of our > engineers had this info for you: > > In addition to -s, we also run with -species 'Mus musculus' for mouse. We > use cross_match. I would expect results of the latest RepeatMasker and > library to be a superset of the old results - the old results should be > recognizable within the new results (maybe with slight differences). > > We also chop up sequence into 500,000-base chunks so we can run RepeatMasker > jobs in parallel on our cluster -- that might cause some differences at the > edges of those chunks. But those differences should not be major. > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > Edward Chuong wrote on 9/20/10 3:30 PM: >> >> Hi, >> I wanted to create an updated Repeatmasker annotation for mm9 assembly >> (the track details say it was last updated in 2007). I tried running >> repeatmasker with the -s setting only, with rmblast, and the latest >> repeatmasker repbase update (June 4 2009). Unfortunately my results >> missed a lot of repeats listed in the public track and in general the >> results were very different. >> >> Any ideas on what may have led to the differences? What engine was >> used (I've seen both cross match and WUblast mentioned on this list)? >> Alternatively are there any plans to update the public mm9 >> repeatmasker track? >> >> Thanks >> -Ed >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
