# 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.

```
$ yap summary -h
usage: yap summary [-h] --output_dir OUTPUT_DIR [--notebook NOTEBOOK]

optional arguments:
  -h, --help            show this help message and exit

Required inputs:
  --output_dir OUTPUT_DIR, -o OUTPUT_DIR
                        Pipeline output directory. (default: None)
  --notebook NOTEBOOK, -nb NOTEBOOK
                        Notebook template for mapping summary, if not
                        provided, will use yap default template. (default:
                        None)
```

This command will do two things

1. 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`
2. It uses a notebook template (or you can provide one by yourself) to generate some plots for visualizing some of the key mapping metrics.

{% hint style="info" %}
You can customize the default notebook template (the one generated by `yap summary`) and provided it to `yap summary` next time.
{% endhint %}

## Evaluate Data Quality

In the mapping summary table, I provide dozens of metrics (as much as I can) for every cell. Many of these metrics are specific and redundant. To evaluate cell quality (for filtering before analysis), we only need some of the [key mapping metrics](https://hq-1.gitbook.io/mc/mapping-metrics/key-mapping-metrics). [Other metrics](https://hq-1.gitbook.io/mc/mapping-metrics/all-mapping-metrics) might be useful for troubleshooting when the library has some quality issues.

## Output

1. The mapping summary table generated at `{output_dir}/stats/MappingSummary.csv.gz`
2. 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.
3. See detailed annotation of mapping metrics on the next page.

![Plate view of mapping metrics](https://1455921630-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-M4FOs0MK_TEUBhXLcyt%2F-MI7LWTFZtedEoVFtB0i%2F-MI7UDE7_ynQ9bGKQgrU%2Fdownload.png?alt=media\&token=5c59dc35-8965-474e-91d7-7598efd58565)