Those are the installation instructions for the single cell workshop at the SIB-Days 2018
First you need to download and install miniconda3:
for linux
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
for mac os
curl https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -o Miniconda3-latest-MacOSX-x86_64.sh
bash Miniconda3-latest-MacOSX-x86_64.sh
Git is going to be used to get the pipeline and snakemake is the pipeline software
conda install git
conda install -c bioconda -c conda-forge snakemake
Clone the worflow locally. The --recursive-submodules
will also download the submodule holding some sample data.
git clone https://github.com/Hoohm/dropSeqPipe
cd dropSeqPipe
git clone https://github.com/Hoohm/sib-days-single-cell.git
This will produce two html reports. One with cell and UMI quality (R1) and one with mRNA (R2) quality.
snakemake --use-conda --cores 2 --directory sib-days-single-cell qc
This will produce a trimmomatic report as well as a few plots linked to filtering
snakemake --use-conda --cores 2 --directory sib-days-single-cell filter
This will produce a STAR html report as well as the yield plot
snakemake --use-conda --cores 2 --directory sib-days-single-cell map
This will produce the final umi_expression_matrix.tsv in the summary folder
snakemake --use-conda --cores 2 --directory sib-days-single-cell extract