Step 1: Setting up the Ensemblex pipeline
In Step 1, we will set up the working directory for the Ensemblex pipeline and decide which version of the pipeline we want to use:
Demultiplexing with prior genotype information
First, create a dedicated folder for the analysis (hereafter referred to as the working directory). Then, define the path to the working directory and the path to ensemblex.pip:
## Create and navigate to the working directory
mkdir working_directory
cd /path/to/working_directory
## Define the path to ensemblex.pip
ensemblex_HOME=/path/to/ensemblex.pip
## Define the path to the working directory
ensemblex_PWD=/path/to/working_directory
Next, we can set up the working directory for demultiplexing with prior genotype information using the following code:
bash $ensemblex_HOME/launch_ensemblex.sh -d $ensemblex_PWD --step init-GT
After running the above code, the working directory should have the following structure
working_directory
├── demuxalot
├── demuxlet
├── ensemblex_gt
├── input_files
├── job_info
│ ├── configs
│ │ └── ensemblex_config.ini
│ ├── logs
│ └── summary_report.txt
├── souporcell
└── vireo_gt
Upon setting up the Ensemblex pipeline, we can proceed to Step 2 where we will prepare the input files for Ensemblex's constituent genetic demultiplexing tools: Preparation of input files
Demultiplexing without prior genotype information
First, create a dedicated folder for the analysis (hereafter referred to as the working directory). Then, define the path to the working directory and the path to ensemblex.pip:
## Create and navigate to the working directory
mkdir working_directory
cd /path/to/working_directory
## Define the path to ensemblex.pip
ensemblex_HOME=/path/to/ensemblex.pip
## Define the path to the working directory
ensemblex_PWD=/path/to/working_directory
Next, we can set up the working directory for demultiplexing without prior genotype information using the following code:
bash $ensemblex_HOME/launch_ensemblex.sh -d $ensemblex_PWD --step init-noGT
After running the above code, the working directory should have the following structure
working_directory
├── demuxalot
├── freemuxlet
├── ensemblex
├── input_files
├── job_info
│ ├── configs
│ │ └── ensemblex_config.ini
│ ├── logs
│ └── summary_report.txt
├── souporcell
└── vireo
Upon setting up the Ensemblex pipeline, we can proceed to Step 2 where we will prepare the input files for Ensemblex's constituent genetic demultiplexing tools: Preparation of input files