pipeline_emptydrops.py
Overview
This pipeline performs the following task:
run emptydrops on the raw output of cellranger
Usage
See Installation and Usage on general information how to use CGAT pipelines.
Configuration
The pipeline requires a configured pipeline.yml
file.
Default configuration files can be generated by executing:
python <srcdir>/pipeline_emptydrops.py config
Input files
The pipeline is run from the cellranger count output (raw_feature_bc_matrix folder).
The pipeline expects a tsv file containing a column named path and a column named sample_id.
‘raw path’ should contain the path to each cellranger path to raw_feature_bc_matrix. ‘sample_id’ is the desired name for each sample (output folder will be named like this).
Dependencies
This pipeline requires: * cgat-core: https://github.com/cgat-developers/cgat-core * R + packages
Pipeline output
The pipeline returns: A list of barcodes passing emptydrops cell identification and a table with barcode ranks including all barcodes (this can be used for knee plots).
Code
- cellhub.pipeline_emptydrops.emptyDrops(infile, outfile)
Run Rscript to run EmptyDrops on each library
- cellhub.pipeline_emptydrops.meanReads(infile, outfile)
Calculate the mean reads per cell
- cellhub.pipeline_emptydrops.full()
Run the full pipeline.