Hi, I wondering if anybody can hep me to generate masked (by RepeatMasker for instance) sequences. I'm currently using Bsgenome to extract sequence from a BED file such as : library(BSgenome.Hsapiens.UCSC.hg18) genome<-Hsapiens FastaSeq<-getSeq(genome,"chr1",start=1000,end=1200, as.character=FALSE) I know that Bsgenome contains masks that can be apply by using : chr1 <- genome$chr1 active(masks(chr1)) <- TRUE So, I'm trying to use it to change the masks of the genome object. But I cannot modify it : active(masks(genome$chr1)) <- TRUE Error in `$<-`(`*tmp*`, "chr1", value = <s4 object="" of="" class="" "maskeddnastring"="">) : no method for assigning subsets of this S4 class Is there a way get the masked sequence with the getSeq function ? Thanks. ------------------------------------------ Eloi Mercier Computational Biology, IRCM 110 av. Des Pins O. Montreal Canada, QC