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RSEM on Helix & Biowulf

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.

Running RSEM on Helix
$ module load rsem
$ rsem-prepare-reference --help

Running RSEM on Biowulf

Set up a batch script called scriptname along the following lines:

#!/bin/bash
#PBS -N rsemjob
#PBS -m be

cd /data/$USER/rsem
module load rsem
rsem command 1
rsem command 2

Submit this job with a command like:

biowulf% qsub -l nodes=1:c24:g24  scriptname

Running RSEM interactively

Allocate an interactive node on Biowulf, and run the process there as in the example below.

biowulf% qsub -I -l nodes=1:c24:g24
qsub: waiting for job 6806847.biobos to start
qsub: job 6806847.biobos ready

[susanc@p2347 ~]$ cd /data/$USER/rsem
[susanc@p2347]$ module load rsem
[susanc@p2347]$ rsem-prepare-reference --help
[susanc@p2347]$ rsem command

Documentation

RSEM user guide