On Thu, Sep 17, 2009 at 8:14 AM, Ivan Gregoretti <ivangreg@gmail.com> wrote:

> 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?
>
>
Well, as rtracklayer said, this track is not representable by WIG, which is
meant to communicate a single data value for a given genomic region (to
generate the bar plots in the UCSC browser, for instance). There aren't any
scores in your file, so why do you want to use WIG?

Michael


> 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
>
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>

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