Dear colleagues, dear Mark, Many thanks for providing the "Repitools "package, it is of great help. There, the function "featureScores" allows for considering mappability for reads via a BSgenome object. Is there any such "mappability-based" BSgenome available, especially for Mus musculus? I could not find one (not even the one mentioned in the Repitools vignette, "BSgenome.Hsapiens36bp.UCSC.hg18mappability_1.0"). In case there is none, I assume I need to forge my own mappability masked version of the Mus musculus genome (or several, for each read length), and provide this as a parameter to the featureScores function? Or is this an overkill and masking just the regions considered in the analysis (e.g., peak regions) is sufficient? Thank you for any hint! Kind regards Markus Dr. Markus Jaritz IMP - Research Institute of Molecular Pathology sessionInof() R version 2.15.2 (2012-10-26) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=de_AT.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=de_AT.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_AT.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.8.3 Biobase_2.18.0 [3] Repitools_1.4.2 BSgenome.Mmusculus.UCSC.mm9_1.3.19 [5] BSgenome_1.26.1 Biostrings_2.26.3 [7] GenomicRanges_1.10.7 IRanges_1.16.6 [9] BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] edgeR_3.0.8 limma_3.14.4 parallel_2.15.2 stats4_2.15.2 [5] tcltk_2.15.2 tools_2.15.2