Well, even if you can't suppress tracklines during bedGraph creation in rtracklayer, it looks like UCSC has updated their bigWig creation utility to skip track lines. (info courtesy of Jeffrey Johnston).
-Chris From: http://genomewiki.ucsc.edu/index.php/Genome_Browser_Software_Features#28_June.2C_2010_v234 28 June, 2010 v234 * PNG 32-bit color for multiWiggles. * More tweaks due to git source control switch. * Ongoing work on multiWiggles. * New CGI: hgTrackRender. * Skip browser and track lines at the beginning of bedGraphs and wigs when creating bigWigs. > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf > Of Chris Seidel > Sent: Friday, August 06, 2010 10:12 AM > To: [email protected] > Subject: [Bioc-sig-seq] rtracklayer - suppress track line > > > Hello, > > I've been using rtracklayer to make bedGraph files from > RLElist objects (which works wonderfully). e.g. a little pseudo code: > > ip <- RLElist(myBigFatChipSEQpipelineResults) > export(ip, "ip.bedGraph") > > I then convert the bedGraph files to bigWigs using the > bedGraphToBigWig command line utility from UCSC. The bigWigs > are binary versions of wig or bedGraph files that are created > from wig or bedGraph data that does not have an initial track > line. However, rtracklayer puts an initial "track line" in > each file by default, that has to be removed for bigWig creation. > > My question is: how do I suppress having a track line in > exported bedGraph data? > > -Chris > > sessionInfo() > R version 2.11.1 > rtracklayer_1.8.1 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
