==== description ====

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 [[anthill_sri011#sbatch example: fastq]] ([[https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf|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





==== software version ====
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==== sbatch example ====
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==== performance tests ====
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