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
