STAR-Fusion

STAR-Fusion.sh

sudo apt install -y libdb-dev axel
sudo cpan DB_File URI::Escape Set::IntervalTree Carp::Assert JSON::XS PerlIO::gzip

cd ~
axel -n 50 -q https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.10/GRCh37_gencode_v19_CTAT_lib_Mar012021.plug-n-play.tar.gz
axel -n 50 -q https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/__genome_libs_StarFv1.10/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play.tar.gz
tar axvf GRCh37_gencode_v19_CTAT_lib_Mar012021.plug-n-play.tar.gz
tar axvf GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play.tar.gz

git --recursive https://github.com/STAR-Fusion/STAR-Fusion.git -b v1.10.0
cd STAR-Fusion
make -j $(nproc)
export PATH=${PWD}:$PATH
cd ~

ulimit -n 65536

STAR \
    --runThreadN $(nproc) \
    --genomeDir ~/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/ \
    --readFilesIn RNA-001_R1.fq.gz RNA-001_R2.fq.gz \
    --readFilesCommand gunzip -c \
    --outFileNamePrefix RNA-001. \
    --outSAMtype BAM Unsorted \
    --outSAMattributes NH HI AS nM NM MD jM jI MC ch XS \
    --outSAMattrRGline "ID:RNA-001" "SM:RNA-001" "PL:Illumina" \
    --outBAMcompression 2 \
    --twopassMode Basic \
          --outSAMstrandField intronMotif \
          --outSAMunmapped Within \
          --chimSegmentMin 12 \
          --chimJunctionOverhangMin 8 \
          --chimOutJunctionFormat 1 \
          --alignSJDBoverhangMin 10 \
          --alignMatesGapMax 100000 \
          --alignIntronMax 100000 \
          --alignSJstitchMismatchNmax 5 -1 5 5 \
          --chimMultimapScoreRange 3 \
          --chimScoreJunctionNonGTAG -4 \
          --chimMultimapNmax 20 \
          --chimNonchimScoreDropMin 10 \
          --peOverlapNbasesMin 12 \
          --peOverlapMMp 0.1 \
          --alignInsertionFlush Right \
          --alignSplicedMateMapLminOverLmate 0 \
          --alignSplicedMateMapLmin 30

STAR-Fusion \
 --genome_lib_dir ~/GRCh38_gencode_v22_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir \
 -J RNA-001.Chimeric.out.junction \
 --output_dir STAR-Fusion-output