A pipeline for fusion gene calling by RNA-seq data and filtering for robust fusion candidates bundled into a Singularity container.
- Singularity installed (version >=3.6)
- 40GB of RAM
- Obtain some files:
- Genome reference in Fasta format (https://www.gencodegenes.org/)
- Gene annotation file in GTF format (https://www.gencodegenes.org/)
- STAR index (build index without '--sjdbGTFfile' and '--sjdbOverhang' parameter, see STAR manual)
- Genomic databases folder as required by FusionCatcher (download newest build: https://sourceforge.net/projects/fusioncatcher/files/data/)
Define the following parameters in the helper script 'RIFTT_part1.sh' before executing:
threads=<integer> # Number of threads for running the detection pipeline
outputfolder=<string> # Path to output folder
genomebuild=<string> # ["hg19", "hg38"]
strandness=<integer> # [0 -> unstranded, 1 -> stranded, 2 -> reversely stranded]
ref=<string> # Path to genome reference file in Fasta format (GENCODE)
anno=<string> # Path to gene annotation file in GTF format (GENCODE)
starindex=<string> # Path to folder containing the STAR index
fcdata=<string> # Path to folder containing the genomic database as required by FusionCatcher
Run the helper script as follows:
./RIFTT_part1.sh <sample_name> <fastq_folder>
Define the following parameters in the helper script 'RIFTT_part2.sh' before executing:
anno=<string> # Path to gene annotation file in GTF format (GENCODE) as used in Part1
outputfolder=<string> # Path to output folder generated by the detection pipeline in Part1
clintable=<string> # Path to clinical information table in Excel format
threads=<integer> # Divisible by 2 !
Run the helper script as follows:
./RIFTT_part2.sh
git clone https://github.com/pkerbs/RIFTT.git <folder>
cd <folder>
sudo singularity build RIFTT.sif RIFTT.def