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anthill_sri011 [2019/07/06 16:05] – tmatejukanthill_sri011 [2023/08/01 01:08] (current) – external edit 127.0.0.1
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 ==== prepare software ==== ==== prepare software ====
-Login to anthill23 and download rMATS along with some test datasets, and gft files((downloading this files will take about 12 minutes)):+Login to anthill23 and download rMATS along with some test datasets, and gft files((downloading this files will take about 3 minutes)):
  
   @anthill23:~$   @anthill23:~$
      
-  mkdir -p ~/anthill23_rmats/{testData,gtf,STARindex}+  mkdir -p ~/anthill23_rmats/{testData,gtf}
   cd ~/anthill23_rmats   cd ~/anthill23_rmats
   wget https://sourceforge.net/projects/rnaseq-mats/files/MATS/rMATS.4.0.2.tgz   wget https://sourceforge.net/projects/rnaseq-mats/files/MATS/rMATS.4.0.2.tgz
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   exit   exit
- 
-==== STAR tool ==== 
-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 
- 
  
 ==== simple test ==== ==== simple test ====
-If above steps ( prepare software, and prepare gsl lib ) finish successfully this simple test should finish with success. It is also done in interactive mode ( +If above steps ( prepare software, and prepare gsl lib ) finish successfully this simple test should finish with success. Do this test in  interactive mode ([[howtouseslurm_000|SLURM, batch and interactive mode]]) :
-[[howtouseslurm_000|SLURM, batch and interactive mode]]) :+
  
   @anthill23:~$   @anthill23:~$
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   srun -J rMATS_test --pty bash -l   srun -J rMATS_test --pty bash -l
      
-  cd /home/users/tmatejuk/anthill23_rmats+  cd /home/users/${USER}/anthill23_rmats
   export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/users/${USER}/anthill23_rmats/gsl-2.4/lib   export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/users/${USER}/anthill23_rmats/gsl-2.4/lib
   python rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rmats.py --b1 testData/b1.txt --b2 testData/b2.txt --gtf gtf/Homo_sapiens.GRCh37.87.gtf --od bam_test -t paired --readLength 50 --cstat 0.0001 --libType fr-unstranded   python rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rmats.py --b1 testData/b1.txt --b2 testData/b2.txt --gtf gtf/Homo_sapiens.GRCh37.87.gtf --od bam_test -t paired --readLength 50 --cstat 0.0001 --libType fr-unstranded
      
   ...   ...
-  #read output and exit when finished+  #read output and exit interactive mode when finished
   exit   exit
  
-==== sbatch example: bam ==== +==== sbatch example ==== 
-Bellow example was taken form [[http://rnaseq-mats.sourceforge.net/user_guide.htm|rMATS User Guide]]. This description assumes that above steps ( prepare software, and prepare gsl lib, simple test ) were done beforehand if not, remember to modify them accordingly. +Bellow example was taken form [[http://rnaseq-mats.sourceforge.net/user_guide.htm|rMATS User Guide]]. This description assumes that above steps ( prepare software, and prepare gsl lib ) were done beforehand if not, remember to modify them accordingly. 
  
-File ''rmats_bam.batch'' . +File ''rmats_test.batch'' . 
  
 <code> <code>
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 #SBATCH --ntasks=4 #SBATCH --ntasks=4
 #SBATCH --mem 4G #SBATCH --mem 4G
 +#SBATCH --job-name rMATS_test
  
 cd /home/users/${USER}/anthill23_rmats cd /home/users/${USER}/anthill23_rmats
 export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/users/${USER}/anthill23_rmats/gsl-2.4/lib export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/users/${USER}/anthill23_rmats/gsl-2.4/lib
  
-python rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rmats.py --b1 b1.txt --b2 b2.txt -gtf gtf/Homo_sapiens.GRCh38.91.gtf -od bam_test -t paired --readLength 50 --cstat 0.0001 --libType fr-unstranded+python rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rmats.py \ 
 + --b1 b1.txt \ 
 + --b2 b2.txt \ 
 + --gtf gtf/Homo_sapiens.GRCh37.87.gtf \ 
 + --od bam_test \ 
 + -t paired \ 
 + --readLength 50 \ 
 + --cstat 0.0001 \ 
 + --libType fr-unstranded
  
 </code> </code>
- 
-Run computation with ''sbatch rmats_bam.batch''. You will find results in  ''/home/users/${USER}/anthill23_rmats/bam_test'' folder. 
  
 ==== performance tests ==== ==== performance tests ====
-...+None. At this time.
  
-<code> 
-... 
-</code> 
  
  
  

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