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jts / ncov-tools

Small collection of tools for performing quality control on coronavirus sequencing data and genomes
MIT License
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Amplicon coverage heatmap plot #106

Closed AnyaKovalenko closed 1 year ago

AnyaKovalenko commented 1 year ago

Dear @jts,

please could you explain how to understand the density (the numbers: -2; -1; 0; 1; 2) on the heatmap amplicon coverage plot? Please see the attached pic. It does not look like the average depth and I am a little bit confused. Thank you again for this amazing tool, love it! best wishes

heatmap_plot

rdeborja commented 1 year ago

Hi Anya, the coverage is log transformed

https://github.com/jts/ncov-tools/blob/2332b92e319ea9fd691dbc914bdc106eaafaa4a0/workflow/scripts/plot/plot_amplicon_coverage_heatmap.R#L124

AnyaKovalenko commented 1 year ago

Hi @rdeborja, thank you mucho!