scRNA-Seq
GitHub Repo
Paper
Current best practices in single-cell RNA-seq analysis: a tutorial
Adjustments to run it on sysbio
login $ git clone https://github.com/theislab/single-cell-tutorial.gitlogin $ cd single-cell-tutorial
Download the example data (This is all on the login node)
mkdir -p data/Haber-et-al_mouse-intestinal-epithelium/cd data/Haber-et-al_mouse-intestinal-epithelium/wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE92nnn/GSE92332/suppl/GSE92332_RAW.tarmkdir GSE92332_RAWtar -C GSE92332_RAW -xvf GSE92332_RAW.targunzip GSE92332_RAW/*_Regional_*wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE92nnn/GSE92332/suppl/GSE92332_Regional_UMIcounts.txt.gzgunzip GSE92332_Regional_UMIcounts.txt.gz
Start the container on a compute node
login $ srun --pty bashsysbio-0 $ ml load singularitysysbio-0 $ singularity exec /scratch/applied-genomics/scrnaseq/single-cell-analysis_210114.sif bash
and then paste the following in to set the environment properly:
export LD_LIBRARY_PATH=/opt/R/lib/R/libexport SHELL=/bin/bashexport TERM=xterm-256colorexport LANG=en_US.UTF-8echo $PATHexport PATH=/opt/python/bin:/opt/R/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
and fire up jupyterlab
jupyter-lab --no-browser --ip=0.0.0.0
- Open another terminal and login to the compute node with port forwarding.
login $ ssh sysbio-1 -L 8888:localhost:8888
- Go back to the first terminal and copy the jupyterlab link into your local browser. It should look something like
http://localhost:8888/lab?token=4d08d209468541b333109fc4f957c8b3d1c97bed59072148
When you finish consider cleaning out the example data to save space on the server