• yap demultiplex output directory, refer to as {output_dir} below.

Cell batches and snakemake

During demultiplex, cells are divided into small batches based on their PCR index. FASTQ files of each batch are saved together in a sub-directory of the {output_dir} . Each of the sub-directory is mapped together in a single job, all the steps that need to be done are written in the {output_dir}/{sub_dir}/Snakefile , a file needed by snakemake, and contain all the commands to map the files in this sub-directory.
Here is a single command used to execute the Snakefile, but you don't need to do this by yourself (see below):
# to map cells in a single sub directory
snakemake \
-d {output_dir}/{sub_dir} \
--snakefile {output_dir}/{sub_dir}/Snakefile \
-j {parallel_cores_to_use_for_this_job}
​What is snakemake?​

Execute snakemake commands

In the {output_dir}/snakemake , you should be able to find a list of snakemake commands like the above, one command for each PCR index sub-directory. You have three ways to execute these commands.

For MiSeq

For NovaSeq

For troubleshooting