Hi there, I'm hoping I can add an easy item to your to-do list, bioc folks? It looks like the BSgenome.Mmusculus.UCSC.mm10 package does not have a RepeatMasker mask at the moment - that would be really useful, to me at least. (I have version BSgenome.Mmusculus.UCSC.mm10_1.3.19) library(BSgenome.Mmusculus.UCSC.mm10) Mmusculus[["chr1"]] 195471971-letter "MaskedDNAString" instance (# for masking) seq: ####################################...########################## ########## masks: maskedwidth maskedratio active names desc 1 3562779 0.01822655 TRUE AGAPS assembly gaps 2 0 0.00000000 TRUE AMB intra-contig ambiguities (empty) all masks together: maskedwidth maskedratio 3562779 0.01822655 thanks, Janet