Hello David, We typically run the doSimpleRepeats.pl automation script. You will also need the bigTrf program to post-process the results of trf into our bed format. We also filter the simpleRepeat BED to keep only items with period <= 12 for masking.
You can get both of those programs as a part of our source downloads. You can find instructions about downloading and installing kent source utilities here: http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads http://genome.ucsc.edu/admin/jk-install.html With the actual source download residing here: http://hgdownload.cse.ucsc.edu/admin/jksrc.zip While we are not in the habit of advising scientific direction on this mailing list one of our developers had this to say about the paper you mention: We go for higher sensitivity at the expense of specificity in our lastz alignments, because we count on the chaining and netting process to restore some specificity. Frith's simulations used lastz and didn't include chaining and netting. Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [email protected]. Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 11/12/10 7:45 AM, David Garfield wrote: > Hi folks, > > I've two general questions. The first is simply a software question. I see > from the FAQ that y'all generally use both Repeat Masker and TRF to deal with > repeats, and that repeats are soft-masked. I know how to soft-mask using > Repeat Masker, but how does one do this on TRF? > > Second, I've seen at least one paper > (http://www.biomedcentral.com/1471-2105/11/80) that strongly suggests that > repeats should be hard masked. Has this (relatively recent) paper changed > your thoughts on hard-masking? > > Many thanks, > > David Garfield > Duke University > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
