Intro to single cell technologies

ACCESSING THE NODE

ssh [email protected]

Type in password.

Data

1. Create a folder

mkdir intro_single_cell
cd intro_single_cell

2. Download data from cellranger 10x website (~ 1 minutes)

curl -O https://cf.10xgenomics.com/samples/cell-exp/3.0.0/pbmc_1k_v3/pbmc_1k_v3_fastqs.tar

3. Look at the copied data that you will use for the exercis

ls

pbmc_1k_v3_fastqs.tar

4. Extract .tar files

tar xvf pbmc_1k_v3_fastqs.tar
cd pbmc_1k_v3_fastqs
ls

5. Look at the fastq file

gunzip -c pbmc_1k_v3_S1_L001_I1_001.fastq.gz > pbmc_1k_v3_S1_L001_I1_001.fastq
head -n 36 pbmc_1k_v3_S1_L001_I1_001.fastq

Fastqc

1. Load module

module load fastqc/0.11.9 mugqic/openjdk-jdk-19

2. Check that you have successuflly load fastqc

fastqc -v

3. Run the tool fastqc to assess the quality of the sequencing

fastqc pbmc_1k_v3_S1_L001_I1_001.fastq.gz

4. To make it easier, let’s look at the FASTQC results on your web browser

mkdir ~/public_html
cp ~/intro_single_cell/pbmc_1k_v3_fastqs/*.html ~/public_html/
chmod -R 755 ~

You can now access your files from a web browser at (by replacing “XX” by your username): https://workshop2021a.vhost37.genap.ca/~micmXX

Cellranger

1. Set cellranger to path

export PATH=/home/*USERNAME*/cellranger-7.0.1:$PATH

2. Check that you have successuflly load cellranger

cellranger --version

3. Run cellranger count (~hours) (change to your username)

cellranger count --id=run_count_1kpbmcs \
   --fastqs=/home/micmXX/intro_single_cell/pbmc_1k_v3_fastqs \
   --sample=pbmc_1k_v3 \
   --transcriptome=/home/micmXX/intro_single_cell/refdata-gex-GRCh38-2020-A

4. You can check the outputs from official website: https://www.10xgenomics.com/resources/datasets/1-k-pbm-cs-from-a-healthy-donor-v-3-chemistry-3-standard-3-0-0

Scanpy

Open the following tutorial codes in colab and copy the file to your account

Tutorial codes:

Tutorial solution codes: