[BioC] rtracklayer laying a track

[Cook, Malcolm]

Just chiming in....

> I should have mentioned that is of course possible to export() the track to
> BED, WIG, GFF, etc, and upload it as a custom track manually. This allows,
> for example, uploading to a user account, so that the session/tracks can be
> shared with others.

This approach can profitably be pursued in combination with the new UCSC capability for "track hubs" (http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html)

--Malcolm



> 
> Michael
> 
> On Wed, Jan 11, 2012 at 8:53 AM, Michael Lawrence <michafla at gene.com>
> wrote:
> 
> > The bug below is caused by the attempt to upload a GRanges, instead of a
> > RangedData. This is basically on its way to being fixed in devel.
> >
> > That said, it won't work anyway, because some time in the last 6 months or
> > so UCSC must have changed its (totally undocumented, internal) interface
> > for uploading tracks, and I have not had the time or desire to reverse
> > engineer it yet again. We could probably ask UCSC for help on this, but
> > this feature is not of use to me nor my employer, so I just can't commit
> > the time to it. Unless someone steps up to help, I'll probably have to
> > disable it.
> >
> > Sorry,
> > Michael
> >
> >
> > On Wed, Jan 11, 2012 at 4:35 AM, simon [guest]
> <guest at bioconductor.org>wrote:
> >
> >>
> >> I could not load a custom track to the UCSC genome browser, so I tried it
> >> according to the rtracklayer vignette and I got also an error. What am I
> >> doing wrong?
> >>
> >> thanks!
> >> simon
> >>
> >>  -- output of sessionInfo():
> >>
> >> > data(targets)
> >> > targetRanges <- IRanges(targets$start, targets$end)
> >> > targetTrack <- with(targets,GRangesForUCSCGenome("hg18", chrom,
> >> targetRanges, strand,name, target))
> >> > session <- browserSession("UCSC")
> >> > track(session, "targets") <- targetTrack
> >> Fehler in genome(seqinfo(x)) :
> >>  Fehler bei der Auswertung des Argumentes 'x' bei der Methodenauswahl
> >> für Funktion 'genome': Fehler in .normargSeqlengths(seqlengths,
> >> seqnames) :
> >>  supplied 'seqlengths' must be a vector
> >>
> >>
> >> R version 2.14.0 (2011-10-31)
> >> Platform: x86_64-unknown-linux-gnu (64-bit)
> >>
> >> locale:
> >>  [1] LC_CTYPE=de_AT.UTF-8          LC_NUMERIC=C
> >>  [3] LC_TIME=de_AT.UTF-8           LC_COLLATE=de_AT.UTF-8
> >>  [5] LC_MONETARY=de_AT.UTF-8       LC_MESSAGES=de_AT.UTF-8
> >>  [7] LC_PAPER=de_AT.UTF-8          LC_NAME=de_AT.UTF-8
> >>  [9] LC_ADDRESS=de_AT.UTF-8        LC_TELEPHONE=de_AT.UTF-8
> >> [11] LC_MEASUREMENT=de_AT.UTF-8    LC_IDENTIFICATION=de_AT.UTF-
> 8
> >>
> >> attached base packages:
> >> [1] stats     graphics  grDevices utils     datasets  methods   base
> >>
> >> other attached packages:
> >> [1] GenomicRanges_1.6.4 IRanges_1.12.5      rtracklayer_1.14.4
> >> [4] RCurl_1.8-0         bitops_1.0-4.1      rj_1.0.2-5
> >>
> >> loaded via a namespace (and not attached):
> >> [1] Biostrings_2.22.0 BSgenome_1.22.0   rj.gd_1.0.2-2     tools_2.14.0
> >> [5] XML_3.6-2         zlibbioc_1.0.0
> >>
> >>
> >> --
> >> Sent via the guest posting facility at bioconductor.org.
> >>
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> >>
> >
> >
> 
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