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--- anthill_sri011 [2019/07/06 19:28] – tmatejuk
+++ anthill_sri011 [2023/08/01 01:08] (current) – external edit 127.0.0.1
@@ Line 10: / Line 10: @@
   @anthill23:~$
-  mkdir -p ~/anthill23_rmats/{testData,gtf,STARindex}
+  mkdir -p ~/anthill23_rmats/{testData,gtf}
   cd ~/anthill23_rmats
   wget https://sourceforge.net/projects/rnaseq-mats/files/MATS/rMATS.4.0.2.tgz
@@ Line 56: / Line 56: @@
   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.
@@ Line 71: / Line 71: @@
 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>
-Run computation with ''sbatch rmats_test.batch''. You will find results in  ''/home/users/${USER}/anthill23_rmats/bam_test'' folder.
 ==== performance tests ====

CRwiki