Before Start
Installation
TECH BACKGROUND
Mapping Pipeline
Prepare
- Prepare PlateInfo & bcl2fastq SampleSheet
- Prepare Mapping Config
  Prepare Reference Files
Demultiplex
Mapping
Mapping Form Cell-Level FASTQ Files
Summary
Mapping Metrics
- Key Mapping Metrics
- All Mapping Metrics
Generate MCDS
Pseudo-bulk
- Methylome Pseudo-bulk
Other
- FAQ
- Changelog

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Mapping Metrics

Columns in the MappingSummary.csv.gz

PreviousSummary NextKey Mapping Metrics

Last updated 4 years ago

YAP gathers many mapping metrics from each step of the pipeline.

To quickly evaluate the cell and library quality, you may start with a few key mapping metrics and recommended cutoffs:

And I also provided the annotation of all mapping matrics in the MappingSummary.csv.gz table.

Key Mapping Metrics

All Mapping Metrics