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
