pipeline_dehash.py
Overview
This pipeline dehashes cells which have multiplexed using hash tag oligos (HTOs).
Usage
See Installation and Usage for general information on how to use cgat pipelines.
Configuration
The pipeline requires a configured pipeline.yml
file.
- Default configuration files can be generated by executing:
cellhub celldb config
Code
- cellhub.pipeline_dehash.gmmDemux(infile, outfile)
Run gmmDemux
- cellhub.pipeline_dehash.gmmAPI(infiles, outfile)
Register the GMM-Demux results on the API
- cellhub.pipeline_dehash.hashCountCSV(infile, outfile)
Make the hash count csv table for demuxEM
- cellhub.pipeline_dehash.demuxEM(infile, outfile)
Run demuxEM
- cellhub.pipeline_dehash.parseDemuxEM(infile, outfile)
Parse the ridiculous output format from demuxEM.
- cellhub.pipeline_dehash.demuxemAPI(infiles, outfile)
Register the demuxEM results on the API