[Bioc-sig-seq] rtracklayer - suppress track line

Chris Seidel seidel at phaget4.org
Fri Aug 6 23:03:40 CEST 2010

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).



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