Hello everybody How do you convert BED formatted files to WIG files?
I tried to do that with rtracklayer but it didn't quite succeed. This is the session's transcript: First, you can download http://dl.getdropbox.com/u/2051155/myRegions.bed, which looks like this chr1 3002444 3002479 + chr1 3002989 3003024 - chr1 3017603 3017638 + chr1 3017879 3017914 - chr1 3018173 3018208 + chr1 3018183 3018218 - chr1 3018183 3018218 - chr1 3019065 3019100 + chr1 3019761 3019796 - chr1 3020044 3020079 - ... Now to R suppressMessages(library(rtracklayer)) myRegions <- import('myRegions.bed') So far so good. Now I try: export(myRegions, 'myRegions.wig', format = 'wig') but I get: Error in export.ucsc(object, con, subformat, ...) : Track not compatible with WIG format: Overlapping features must be on separate strands and every feature width must be positive I seems that the error message is a feature rather than a bug. My interpretation is that export() does not like records like lines 6 and 7: chr1 3018183 3018218 - chr1 3018183 3018218 - So, how do you convert BED to WIG in your everyday work? Thank you, Ivan > sessionInfo() R version 2.9.2 (2009-08-24) x86_64-redhat-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.4.0 RCurl_0.94-1 loaded via a namespace (and not attached): [1] Biobase_2.4.0 Biostrings_2.12.0 BSgenome_1.12.0 IRanges_1.2.0 [5] tools_2.9.2 XML_2.3-0 Ivan Gregoretti, PhD National Institute of Diabetes and Digestive and Kidney Diseases National Institutes of Health 5 Memorial Dr, Building 5, Room 205. Bethesda, MD 20892. USA. Phone: 1-301-496-1592 Fax: 1-301-496-9878 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
