Run the pipeline with demultiplexning in Uppsala:
git clone https://github.com/clinical-genomics-uppsala/Twist_RNA.git .
git checkout develop
module add snakemake
module add slurm-drmaa
module add singularity
snakemake -p -j 1 --drmaa "-A wp1 -p core -n 1 -t 2:00:00 " -s ./src/Snakemake/rules/Twist_RNA_yaml/Twist_RNA_yaml.smk
snakemake -p -j 80 --drmaa "-A wp1 -p core -n {cluster.n} -t {cluster.time}" -s ./Twist_RNA.smk --use-singularity --singularity-args "--bind /data --bind /projects --bind /scratch " --cluster-config Config/Slurm/cluster.json
Run the pipeline from Fastq-files anywhere:
cd <analysis_dir>
git clone https://github.com/clinical-genomics-uppsala/Twist_RNA.git .
git checkout develop
Create samples.tsv with the following format:
Sample_name1 Path/to/fastq/R1.fastq.gz Path/to/fastq/R2.fastq.gz
Sample_name2 Path/to/fastq/R1.fastq.gz Path/to/fastq/R2.fastq.gz
Adapt Config/Pipeline/configdefaults201012.yaml to your system by providing paths to the references needed
Create Twist_RNA.yaml with the following command:
snakemake -p -j 1 --drmaa "-A wp1 -p core -n 1 -t 2:00:00 " -s ./src/Snakemake/rules/Twist_RNA_yaml/Twist_RNA_yaml_fastq.smk
Run pipeline with a command similar to this with bind points and -A adapted to your system: #Use screen or similar!
snakemake -p -j 80 --drmaa "-A wp1 -p core -n {cluster.n} -t {cluster.time}" -s ./Twist_RNA.smk --use-singularity --singularity-args "--bind /data --bind /projects --bind /scratch " --cluster-config Config/Slurm/cluster.json
Reference files: #Or get them directly from us to get exactly the same versions
Arriba Star reference files (Needs 8 cores and 45Gb memory):
mkdir /path/to/references
singularity exec -B /path/to/references:/references docker://uhrigs/arriba:2.1.0 download_references.sh GRCh37+RefSeq
Star-fusion reference files:
Download from: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.9/
FusionCatcher:
See instructions on Fusioncatcher github or follow commands in:
https://github.com/ndaniel/fusioncatcher/blob/master/data/download-human-db.sh