multiple samples needed?
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monikaramos commented
Can I run this on one sample?
acvill commented
Can I run this on one sample?
Yes. combine_bracken_outputs.py will take a single sample as input, and the output can be used to create a single-sample relative abundance bar plot with the bracken_plot shiny app. Note that the app won't work with the raw bracken output, which lacks a column-encoded sample name.