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software

RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides an user-friendly interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, variable-length reads and RSPD estimation. In addition, it provides posterior mean and 95% credibility interval estimates for expression levels. For visualization, It can generate BAM and Wiggle files in both transcript-coordinate and genomic-coordinate. Genomic-coordinate files can be visualized by both UCSC Genome browser and Broad Institute's Integrative Genomics Viewer (IGV). Transcript-coordinate files can be visualized by IGV. RSEM also has its own scripts to generate transcript read depth plots in pdf format. The unique feature of RSEM is, the read depth plots can be stacked, with read depth contributed to unique reads shown in black and contributed to multi-reads shown in red. In addition, models learned from data can also be visualized. Last but not least, RSEM contains a simulator.

Software and its description is available at : https://github.com/deweylab/RSEM
software instalation @anthill23

Before you can use RSEM software at anthill you need to install it.

Firstly login to anthill23.cent1.uw.edu.pl and open an interactive session :

srun -p test --pty bash -l

Then run following commands ( it will take less than 12 minutes ) :

mkdir -p ~/anthill23_soft/RSEM
cd ~/anthill23_soft/RSEM
wget https://github.com/deweylab/RSEM/archive/master.zip
unzip master.zip
cd RSEM-master
make -j ${SLURM_NTASKS}
make ebseq
make install DESTDIR=/home/users/${USER}/anthill23_soft/RSEM prefix=/software

As a result you will get RSEM executable binary in :

/home/users/${USER}/anthill23_soft/RSEM/software/bin/

batch file template

First login to anthill23.cent1.uw.edu.pl.

Then create job file (batch), and save it as i.e. rsem_testrun.batch .

#!/bin/bash -l
#SBATCH --job-name=RSEM_test
#SBATCH --partition=long
#SBATCH --ntasks=2
#SBATCH --mem 2048M

#RSEM executable path
RSEMBINPATH=/home/users/${USER}/anthill23_soft/RSEM/software/bin/
 
#printout some info
echo "RSEM anthill test"
echo "date: " `date`
echo "node_name: " `hostname`

#run rsem-prepare-reference program with --help argument
${RSEMBINPATH}/rsem-prepare-reference --help

Then run created batch file ( value 60622 is jobID, it will be different in each job submission):

[anteater@anthill23 tests]$ sbatch rsem_testrun.batch 
Submitted batch job 60622

Depending on availability of computing nodes your job should end in just few moments, and batch output will be located in slurm-60622.out file.