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anthill_sri011 [2019/07/06 13:47] – 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 dataset, and gft files:+Login to anthill23 and download rMATS along with some test datasets, and gft files((downloading this files will take about 3 minutes)):
  
   @anthill23:~$   @anthill23:~$
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   wget ftp://ftp.ensembl.org/pub/grch37/current/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz   wget ftp://ftp.ensembl.org/pub/grch37/current/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz
   gunzip Homo_sapiens.GRCh37.87.gtf.gz   gunzip Homo_sapiens.GRCh37.87.gtf.gz
-  wget ftp://ftp.ensembl.org/pub/release-91/gtf/homo_sapiens/Homo_sapiens.GRCh38.91.gtf.gz 
-  gunzip Homo_sapiens.GRCh38.91.gtf.gz 
  
 ==== prepare gsl lib ==== ==== prepare gsl lib ====
-rMATS uses gsl library that need to be prepared separately((takes about five minutes)). This library have to be compiled on computing node, so it is done in interactive mode ( +rMATS uses gsl library that need to be prepared separately((takes about five minutes)). This library have to be compiled on computing node, so it is done in interactive mode ([[howtouseslurm_000|SLURM, batch and interactive mode]]) :
-[[howtouseslurm_000|SLURM, batch and interactive mode]]) :+
  
   @anthill23:~$   @anthill23:~$
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 ==== 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 [[rMATS User Guide|http://rnaseq-mats.sourceforge.net/user_guide.htm]]. 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-turbo-xxx-UCSx/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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