coverage plot about covid-19-signal HOT 9 CLOSED

Would the HiSAT2 result then substitute the bedtools genomecov -d files since both provide a per-base coverage file? Or perhaps the broader question becomes do we cut the bedtools to reduce the number of jobs; knock two birds with one stone?

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I would keep the pipeline as is but use the coverage/depth.text file to make a plot

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Ah, I might be mixing up output files, the depth.txt is from bedtools.

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Examples in log scale:

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Did you generate this example plot with any particular plotting library/tool?

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Integrative Genomics Viewer is how the example one was made.

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Jared's tool does a good job of creating a plot similar to this.

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I modified the postprocessing script to generate coverage plots like the one below. Maybe it would be useful to have it run in the core pipeline, instead of in the postprocessing script?

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Let's use @kmsmith137's plots in the core pipeline.

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