Graphic tracks UCSC genome browser
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@fenton-christopher-graham-5504
Last seen 4.9 years ago
Have just been asked to produce a relatively complex graphic track from a transcriptome sequencing population study. Basically the investigator would like to see the distribution of the transcriptomic data. for example, 1st quartile, mean, 3 quartile, max for each transcript. Has anyone done anything similar? Should I separate the tracks, min-max, 1st-mean-3rd? Which file format is best suited for this representation of the data? Chris
Sequencing Sequencing • 844 views
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@michael-lawrence-3846
Last seen 2.9 years ago
United States
You could use the rtracklayer BigWig export to create a separate track for each statistic. Michael On Fri, Dec 7, 2012 at 1:17 AM, Fenton Christopher Graham < christopher.fenton@uit.no> wrote: > Have just been asked to produce a relatively complex graphic track from a > transcriptome sequencing population study. > Basically the investigator would like to see the distribution of the > transcriptomic data. > for example, 1st quartile, mean, 3 quartile, max for each transcript. > > Has anyone done anything similar? > Should I separate the tracks, min-max, 1st-mean-3rd? > Which file format is best suited for this representation of the data? > > Chris > > _______________________________________________ > 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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On Fri, Dec 7, 2012 at 7:29 AM, Michael Lawrence <lawrence.michael@gene.com>wrote: > You could use the rtracklayer BigWig export to create a separate track for > each statistic. Michael > > > On Fri, Dec 7, 2012 at 1:17 AM, Fenton Christopher Graham < > christopher.fenton@uit.no> wrote: > > > Have just been asked to produce a relatively complex graphic track from a > > transcriptome sequencing population study. > > Basically the investigator would like to see the distribution of the > > transcriptomic data. > > for example, 1st quartile, mean, 3 quartile, max for each transcript. > > > > Has anyone done anything similar? > > Should I separate the tracks, min-max, 1st-mean-3rd? > > Which file format is best suited for this representation of the data? > You might also look into other visualization approaches that might display the quantitative information a little more fully and succinctly. For example, you could, for example, build a small application using the relatively newly released shiny package displaying a histogram or multiple density plots of the data for a given transcript. http://www.rstudio.com/shiny/ Sean [[alternative HTML version deleted]]
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