rtracklayer laying a track
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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 f??r 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.
rtracklayer rtracklayer • 1.1k views
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@michael-lawrence-3846
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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@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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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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. Michael On Wed, Jan 11, 2012 at 8:53 AM, Michael Lawrence <michafla@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@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. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]
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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 > >> f??r 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. > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor at r-project.org > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > > > > > > [[alternative HTML version deleted]]
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Wow, that's a neat find. Track hubs seem very similar to IGB Quickload (which rtracklayer already supports). The abstractions are already in place to make this alternate implementation easy. Assuming the user has access to a web accessible directory, this would avoid any reliance on the internals of the UCSC web site. Thanks a lot for that tip, Michael On Wed, Jan 11, 2012 at 11:57 AM, Cook, Malcolm <mec@stowers.org> wrote: > 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@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@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. > > >> > > >> _______________________________________________ > > >> Bioconductor mailing list > > >> Bioconductor@r-project.org > > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > > >> Search the archives: > > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > >> > > > > > > > > > > [[alternative HTML version deleted]] > > [[alternative HTML version deleted]]
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thank you for the information, indeed I could execute my scripts and view the results with the custom tracks in the genome browser a couple of months ago that is why I was asking. bw, simon [[alternative HTML version deleted]]
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Sure, I understand. Would you be able to make use of the track hub feature pointed out by Malcolm? I could aim to incorporate that into rtracklayer by the next Bioc release. Michael On Fri, Jan 13, 2012 at 12:02 AM, Simon Schaffrr <schaffrr@gmail.com> wrote: > thank you for the information, indeed I could execute my scripts and view > the results with the custom tracks in the genome browser a couple of months > ago that is why I was asking. > > bw, > simon > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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