/sib-days-single-cell

Files related to the single cell workshop given at the sib-days 2018

Primary LanguageShell

Installation instructions

Those are the installation instructions for the single cell workshop at the SIB-Days 2018

Step 1: Download and install miniconda3

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

Step 2: Install snakemake and Git

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

Step 3: Clone the workflow

Clone the worflow locally. The --recursive-submodules will also download the submodule holding some sample data.

git clone https://github.com/Hoohm/dropSeqPipe

Step 4: Clone the sample data

cd dropSeqPipe
git clone https://github.com/Hoohm/sib-days-single-cell.git

Hands on instructions (following the flow of the pre-processing presentation)

Step 1: Sequencing quality

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

Step 2: Filtering

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

Step 3: Mapping

This will produce a STAR html report as well as the yield plot

snakemake --use-conda --cores 2 --directory sib-days-single-cell map

Step 4: Demultiplexing and extracting

This will produce the final umi_expression_matrix.tsv in the summary folder

snakemake --use-conda --cores 2 --directory sib-days-single-cell extract