How to plot the coverage for each amplicon across the samples?

Question

[macgenome]

Hi everybody, I have sequenced a virus using the amplicon approach (similar to the ARTIC for SARS-CoV-2) using 28 pairs of primers. I would like to plot the coverage for each amplicon across the samples in order to understand which amplicon is not amplified. What should I do? Do you have any tools you may suggest me to obtain the tables for the plot? I would like to obtain a figure similar to the one in this pre-print (Fig 3) https://www.biorxiv.org/content/10.1101/2020.06.16.154286v1.full. All the best

[ml21]

Hello, I am needing to do something similar for a different application. Did you manage to work out how to do it? :) Thanks!

Answer 1

[JC]

Those plots are combination of some R packs (GenomicRanges), check http://www.sthda.com/english/wiki/visualize-ngs-data-with-r-and-bioconductor

[macgenome]

Thank you for the link!