CRwiki

File http://rmaps.cecsresearch.org/STAR/STARindex.tgz referenced in rMATS is no longer available. So to be able to test fast examples we need to generate an index of the reference genome ourselfs http://people.duke.edu/~ccc14/duke-hts-2018/bioinformatics/genome_prep.html .

Use bellow to install STAR software :

@anthill23:~$

srun -J star_compile --pty bash -l

cd ~/anthill23_rmats/
wget https://github.com/alexdobin/STAR/archive/2.7.1a.tar.gz
tar xzf 2.7.1a.tar.gz
cd STAR-2.7.1a
cd source
make STAR

exit

Use bellow to generate index required to run sbatch example: fastq (more info how to use STAR ) .

@anthill23:~$

srun -J create_index -N1 -n16 --mem 220G --pty bash -l

cd ~/anthill23_rmats/gtf
wget ftp://ftp.ensembl.org/pub/release-91/gtf/homo_sapiens/Homo_sapiens.GRCh38.91.gtf.gz
gunzip Homo_sapiens.GRCh38.91.gtf.gz
wget ftp://ftp.ensembl.org/pub/release-91/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz
gunzip Homo_sapiens.GRCh38.dna.toplevel.fa.gz

BASE_DIR="/home/users/${USER}/anthill23_rmats/"
STAR_BIN="${BASE_DIR}/STAR-2.7.1a/source/"
GENOME_DIR="${BASE_DIR}/gtf/"
FASTA="${BASE_DIR}/gtf/Homo_sapiens.GRCh38.dna.toplevel.fa"
GTF="${BASE_DIR}/gtf/Homo_sapiens.GRCh38.91.gtf"
STAR_OUT="${BASE_DIR}/STARindex/"

#??? OMP_NUM_THREADS ???

${BASE_DIR}/STAR-2.7.1a/source/STAR \
  --runThreadN 16 \
  --limitGenomeGenerateRAM 214748364800 \
  --runMode genomeGenerate \
  --genomeDir $GENOME_DIR \
  --genomeFastaFiles ${FASTA} \
  --sjdbGTFfile ${GTF} \
  --outFileNamePrefix ${STAR_OUT}/genome_ \
  --genomeSAindexNbases 11

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