run CICERO (Clipped-reads Extended for RNA Optimization) is an assembly-based algorithm to detect diverse classes of driver gene fusions from RNA-seq.

CICERO.sh

## first, STAR
## second, RemoveDuplicates

cd ~
mkdir CICERO-reference
cd CICERO-reference
mkdir GRCh37-lite
cd  GRCh37-lite
wget -O reference.tar.gz https://zenodo.org/record/3839940/files/reference.tar.gz?download=1
tar axvf reference.tar.gz
cd ..
mkdir GRCh38_no_alt
cd GRCh38_no_alt
wget -O reference.tar.gz https://zenodo.org/record/3894740/files/reference.tar.gz?download=1
tar axvf reference.tar.gz
cd ..
sudo chmod -R a+r .
cd ~

sudo docker pull mnedmonson/public:rnapeg
sudo docker pull ghcr.io/stjude/cicero:v1.5.1

sudo docker run \
 -v ~/CICERO-reference/GRCh37-lite/reference:/reference \
 -v ~/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir:/fasta \
 -v ${PWD}:/results \
 mnedmonson/public:rnapeg RNApeg.sh \
 -b /results/RNA-001.bam \
 -f /fasta/ref_genome.fa \
 -r /reference/Homo_sapiens/GRCh38_no_alt/mRNA/RefSeq/refFlat.txt

sudo docker run \
 -v ~/CICERO-reference/GRCh38_no_alt/reference:/reference \
 -v ${PWD}:/results \
 ghcr.io/stjude/cicero:v1.5.1  \
 Cicero.sh -n $(nproc) \
 -b /results/RNA-001.bam \
 -g GRCh38_no_alt \
 -r /reference \
 -o /results \
 -j /results/RNA-001.bam.junctions.tab.shifted.tab