Summary
Input
The {output_dir}
after mapping.
Generate MappingSummary
Once all the snakemake commands finished successfully, you can execute a single command to get the final mapping summary of your library.
This command will do two things
It creates a total mapping summary file that contains all the mapping metrics for all cells in your library. This file will be saved into
{output_dir}/stats/MappingSummary.csv.gz
It uses a notebook template (or you can provide one by yourself) to generate some plots for visualizing some of the key mapping metrics.
Evaluate Data Quality
Output
The mapping summary table generated at
{output_dir}/stats/MappingSummary.csv.gz
Jupyter notebook and HTML file of some visualization of the mapping metrics, also located in the same directory. The plate view uses the cell's original 384-plate position as coordinates and color code mapping metrics.
See detailed annotation of mapping metrics on the next page.
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