Browse Reads with Bioconductor¶
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Bioconductor provides a convenient way to browse regions of the genome.
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")
To make use of this upon your own data:
- First, load your data into Google Genomics. See Load Data into Google Genomics for more detail as to how to do this.
- 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.
- Update the parameters to the
getReadscall the example above to match that of your data and desired genomic region to view.