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rsem-software [2015/07/23 17:00]
joguya
rsem-software [2018/11/18 11:02] (current)
aorth
Line 1: Line 1:
 ====== RSEM ====== ====== RSEM ======
-RSEM(RNA-Seq by Expectation-Maximization) ​is an accurate quantification of gene and isoform expression from RNA-Seq data.+RSEM is a software package for estimating ​gene and isoform expression ​levels ​from RNA-Seq data.
  
-  * Version: 1.2.21+  * Version: 1.3.1
   * Added: February, 2015   * Added: February, 2015
-  * Updated: ​July2015 +  * Updated: ​November2018 
-  * Link: http://​deweylab.biostat.wisc.edu/rsem/+  * Link: https://​deweylab.github.io/RSEM/
  
 === Usage === === Usage ===
-  * Show all available versions ​of RSEM<​code>​module avail RSEM</​code>​ +Show all available versions
-  ​* ​Load RSEM module: <​code>​module load RSEM/1.2.21</​code>​+ 
 +<​code>​module avail RSEM</​code>​ 
 + 
 +Load one version into your environment: 
 +<​code>​module load RSEM/1.3.1</​code>​
  
 === Installation === === Installation ===
-  *Download & build/​compile it<​code>​ +Notes from the sysadmin during installation:​ 
-wget http://deweylab.biostat.wisc.edu/rsem/src/rsem-1.2.21.tar.gz + 
-tar -xvf rsem-1.2.21.tar.gz  +<​code>​$ cd /tmp 
-cd rsem-1.2.21 +wget https://github.com/deweylab/RSEM/archive/v1.3.1.tar.gz 
-scl enable devtoolset-2 bash +tar xf v1.3.1.tar.gz 
-module load bowtie2 +cd RSEM-1.3.1 
-make +$ sudo yum install gcc-c++ 
-sudo mkdir /​export/​apps/​RSEM/​1.2.21/ +make 
-sudo cp -r . /​export/​apps/​RSEM/​1.2.21+sudo mkdir -p /​export/​apps/​RSEM/​1.3.1 
-</​code>​+sudo chown aorth /​export/​apps/​RSEM/​1.3.
 +$ make prefix=/export/​apps/​RSEM/​1.3.1 install 
 +$ sudo chown -R root:root /​export/​apps/​RSEM/​1.3.1</​code>​
rsem-software.1437660035.txt.gz · Last modified: 2015/07/23 17:00 by joguya