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 <seidel@phaget4.org> 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: bioc-sig-sequencing-bounces@r-project.org
> > [mailto:bioc-sig-sequencing-bounces@r-project.org] On Behalf
> > Of Chris Seidel
> > Sent: Friday, August 06, 2010 10:12 AM
> > To: bioc-sig-sequencing@r-project.org
> > 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
>
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