Plot a represenation of long read alignments in a region of interest
- These plots attempt to visualize a mapping from “read-space” (the actual piece of DNA sequenced) to “reference-space” (where the portions of the read align to the reference genome).
Rscript longReadPlot.R --bam $bam --region $region --output $output
--bam: bam file to plot--region: region to plot in ucsc format e.g. chr17:10958130-11017414--output: output image file name, the extension determines the output format (png, pdf, etc.)--debug: debug mode, if set to debug mode a tsv file of the alignments will be created
- Clone the repository and run the longReadPlot.R script directly via
Rscript
- Need to have R and the required packages installed
- Use the container image to run the script via docker or singularity
https://github.com/jlanej/long-read-plot/pkgs/container/long-read-plot
- Just need to have docker or singularity installed
A parameterized example of how to use the plotting script can be found in the example directory here https://github.com/jlanej/long-read-plot/blob/main/examples/example.NA19240.sh. This script uses singularity to run the plotting script in a container.
The example image above in this readme can be created by running the following command:
#!/bin/bash
#This example bam is packaged within image, bind the bam's directory for non-packaged bams
bam=/long-read-plot/examples/NA19240_2020_merged.ccs.hg38.aligned.chr17_10958130_11017414.bam
region=chr17:10958130-11017414
outputDir=$HOME/tmp/NA19240_output/
output=$outputDir/NA19240_2020_merged.ccs.hg38.aligned.chr17_10958130_11017414.png
singularity run --containall \
--bind "$outputDir/" \
"docker://ghcr.io/jlanej/long-read-plot:main" \
Rscript /long-read-plot/longReadPlot.R --bam $bam --output $output --region $region --debug