BraCeR - reconstruction of B cell receptor sequences from single-cell RNA-seq data.

Installation¶

The following will install parts of BraCeR in the following locations:

Content of the BraCeR Git repository: $HOME/bracer
Virtual Python environment: $HOME/venv_bracer
Transcriptome databases for Kallisto: /scratch/$USER/GRCh38 and /scratch/$USER/GRCm38

However, it could also be structured differently. Please refer to our Storage and file management page for a comparison of the different storage types available.

# BraCeR installation instructions as of August 2022.
# Get bracer
cd ~/
git clone https://github.com/Teichlab/bracer.git

# load modules
module load StdEnv/2020
module load python/3.8
module load gcc/9.3.0 bowtie2/2.4.1 bowtie/1.3.0 trinity/2.14.0 samtools/1.15.1
module load igblast/1.17.0   blast+/2.12.0    kallisto/0.46.1
module load samtools/1.15.1  jellyfish/2.3.0
module load salmon/1.7.0     fastqc/0.11.9

# create a virtualenv for bracer and install dependencies
virtualenv --no-download  ~/venv_bracer
source ~/venv_bracer/bin/activate
pip install --no-index biopython==1.77
pip install --no-index -r ~/bracer/requirements.txt
pip install --no-index graphviz

# install bracer into venv
cd ~/bracer/
python setup.py install

# install Trim Galore
pusd $VIRTUAL_ENV/
## download and extract Trim Galore
wget https://github.com/FelixKrueger/TrimGalore/archive/refs/tags/0.6.7.tar.gz \
     -O TrimGalore-0.6.7.tar.gz
tar xzf TrimGalore-0.6.7.tar.gz
# tweak the Perl "hashbang":
sed -i 's&#!/usr/bin/perl&#!/usr/bin/env perl&'  TrimGalore-0.6.7/trim_galore
# copy  the trim_galore Perl-script into the virtualenv's "bin" directory:
cp  TrimGalore-0.6.7/trim_galore  $VIRTUAL_ENV/bin
popd

# Base transcriptomes for Kallisto
# adapted https://github.com/Teichlab/bracer#base-transcriptomes-for-kallisto
# to download from https://www.gencodegenes.org/
# This downloads the latest releases 41 (Human) and M30 (mouse) respectively
cd ~/scratch
mkdir GRCh38
cd GRCh38
wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_41/gencode.v41.transcripts.fa.gz
gunzip gencode.v41.transcripts.fa.gz
python3 ~/bracer/docker_helper_files/gencode_parse.py gencode.v27.transcripts.fa
cd ..

mkdir GRCm38
cd GRCm38
wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M30/gencode.vM30.transcripts.fa.gz
gunzip gencode.vM30.transcripts.fa.gz
python3 ~/bracer/docker_helper_files/gencode_parse.py gencode.vM30.transcripts.fa
cd ~/

Running BraCeR¶

Note

Make sure to replace USERNAME with your username in the bracer.conf.

bracer.conf¶

bracer.conf

# Configuration file for BraCeR#

[tool_locations]
# paths to tools used by BraCeR for alignment, quantitation, etc
# As all tools are in the PATH this section can be empty

[trinity_options]
# line below specifies maximum memory for Trinity Jellyfish component. 
# Set it appropriately for your environment.
max_jellyfish_memory = 15G

# undocumented option
trinity_version = 2

[kallisto_transcriptomes]
Hsap = /scratch/USERNAME/GRCh38
Mmus = /scratch/USERNAME/GRCm38

[bracer_location]
#Path to where BraCeR was originally installed
bracer_path = /home/USERNAME/bracer/

Jobscript¶

bracer_job.sh

```bash

!/bin/bash¶

SBATCH --time=0-00:30 # 30 minutes (D-hh:mm)¶

SBATCH --cpus-per-task=4¶

SBATCH --mem-per-cpu=4000M¶

module load StdEnv/2020 module load gcc/9.3.0 bowtie2/2.4.1 bowtie/1.3.0 trinity/2.14.0 samtools/1.15.1 module load igblast/1.17.0 blast+/2.12.0 kallisto/0.46.1 module load samtools/1.15.1 jellyfish/2.3.0 module load salmon/1.7.0 fastqc/0.11.9

echo "---------------------------------------------------------------------" module -w 80 list echo "---------------------------------------------------------------------"

source ~/venv_bracer/bin/activate

bracer assemble --ncores ${SLURM_CPUS_PER_TASK:-1} --config_file bracer.conf \ my_cell_name ./my_output_directory/ file_001.fastq file_002.fastq \