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anthill_sri011 [2019/07/06 19:19] – 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
  
-==== sbatch example: ====+==== 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 ) 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. 
  
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 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.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 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_test.batch''. You will find results in  ''/home/users/${USER}/anthill23_rmats/bam_test'' folder. 
  
 ==== performance tests ==== ==== performance tests ====
 None. At this time. None. At this time.
  
-<code> 
-... 
-</code> 
  
  
  
anthill_sri011.1562433591.txt.gz · Last modified: 2023/08/01 06:38 (external edit)

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