That's good news, since the track line is specified as a required element of the bedGraph format. Also note that you can directly output bigwig with rtracklayer (except on Windows). Just export() with a file extension of 'bw'. See help(export.bw).
Michael On Fri, Aug 6, 2010 at 2:03 PM, Chris Seidel <[email protected]> wrote: > 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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
