Dear all, has anybody noticed that extendReads() seems to extend reads on the minus strand below zero? For example, if I have a 36 nt read starting at base 215 on the minus strand, and use extendReads(aln, seqLen=350), aln being an object of class AlignedRead, my resulting extended read runs from base -96 to base 251. I loosely remember this being an issue discussed on one of the BioC or bio-sig-seq mailing lists, but I'm not sure if it was about this specific function and I couldn't find the thread any more - I'm sorry if this has been discussed already and would be thankful for a hint. This is my sessionInfo(): > sessionInfo() R version 2.10.0 (2009-10-26) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=de_DE.UTF-8 [7] LC_PAPER=de_DE.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] chipseq_0.3.1 ShortRead_1.4.0 lattice_0.17-26 BSgenome_1.14.1 [5] Biostrings_2.14.5 IRanges_1.4.9 loaded via a namespace (and not attached): [1] Biobase_2.6.0 grid_2.10.0 hwriter_1.1 tools_2.10.0 Best, Nora