Browse Reads with BioconductorΒΆ

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Bioconductor provides a convenient way to browse regions of the genome. browse-reads

require(ggbio)
require(GoogleGenomics)

GoogleGenomics::authenticate("/PATH/TO/YOUR/client_secrets.json")

galignments <- getReads(readGroupSetId="CMvnhpKTFhDnk4_9zcKO3_YB", chromosome="17",
                        start=41218200, end=41218500, converter=readsToGAlignments)
strand_plot <- autoplot(galignments, aes(color=strand, fill=strand))
coverage_plot <- ggplot(as(galignments, "GRanges")) + stat_coverage(color="gray40",
                                                    fill="skyblue")
tracks(strand_plot, coverage_plot, xlab="chr17")

A more extensive example of read browsing with Bioconductor is documented towards the end of codelab Data Analysis using Google Genomics.

To make use of this upon your own data:

  1. First, load your data into Google Genomics. See Load Data into Google Genomics for more detail as to how to do this.
  2. If you do not have them already, install the necessary Bioconductor packages. See Using Bioconductor for more detail as to how to do this. Alternatively, you can Run Bioconductor on Compute Engine.
  3. Update the parameters to the getReads call the example above to match that of your data and desired genomic region to view.

Have feedback or corrections? All improvements to these docs are welcome! You can click on the “Edit on GitHub” link at the top right corner of this page or file an issue.

Need more help? Please see https://cloud.google.com/genomics/support.