Hi, where do I find the chain files, e.g. hg18ToHg19.over.chain? Thanks Wim > sessionInfo() R version 2.15.2 (2012-10-26) Platform: i686-pc-linux-gnu (32-bit) 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=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 [7] LC_PAPER=C 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] GenomicFeatures_1.10.1 AnnotationDbi_1.20.3 Biobase_2.18.0 [4] rtracklayer_1.18.2 GenomicRanges_1.10.6 IRanges_1.16.4 [7] BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] biomaRt_2.14.0 Biostrings_2.26.3 bitops_1.0-5 BSgenome_1.26.1 [5] colorspace_1.2-1 compiler_2.15.2 DBI_0.2-5 dichromat_2.0-0 [9] digest_0.6.2 ggplot2_0.9.3 grid_2.15.2 gtable_0.1.2 [13] labeling_0.1 MASS_7.3-23 munsell_0.4 parallel_2.15.2 [17] plyr_1.8 proto_0.3-10 RColorBrewer_1.0-5 RCurl_1.95-3 [21] reshape2_1.2.2 Rsamtools_1.10.2 RSQLite_0.11.2 scales_0.2.3 [25] stats4_2.15.2 stringr_0.6.2 tools_2.15.2 XML_3.95-0.1 [29] zlibbioc_1.4.0 [[alternative HTML version deleted]]

http://hgdownload.soe.ucsc.edu/downloads.html search in that page for "chain" On Sat, Mar 2, 2013 at 2:05 PM, Wim Kreinen <wkreinen@gmail.com> wrote: > Hi, > > where do I find the chain files, e.g. hg18ToHg19.over.chain? > > Thanks Wim > > > sessionInfo() > R version 2.15.2 (2012-10-26) > Platform: i686-pc-linux-gnu (32-bit) > > 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=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 > [7] LC_PAPER=C 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] GenomicFeatures_1.10.1 AnnotationDbi_1.20.3 Biobase_2.18.0 > [4] rtracklayer_1.18.2 GenomicRanges_1.10.6 IRanges_1.16.4 > [7] BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] biomaRt_2.14.0 Biostrings_2.26.3 bitops_1.0-5 > BSgenome_1.26.1 > [5] colorspace_1.2-1 compiler_2.15.2 DBI_0.2-5 > dichromat_2.0-0 > [9] digest_0.6.2 ggplot2_0.9.3 grid_2.15.2 > gtable_0.1.2 > [13] labeling_0.1 MASS_7.3-23 munsell_0.4 > parallel_2.15.2 > [17] plyr_1.8 proto_0.3-10 RColorBrewer_1.0-5 > RCurl_1.95-3 > [21] reshape2_1.2.2 Rsamtools_1.10.2 RSQLite_0.11.2 > scales_0.2.3 > [25] stats4_2.15.2 stringr_0.6.2 tools_2.15.2 > XML_3.95-0.1 > [29] zlibbioc_1.4.0 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]