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Sailfish on Biowulf

Sailfish is a software package for inference of transcript abundances from RNA-seq data. Sailfish was developed by Rob Patro, and Carl Kingsford at the Lane Center for Computational Biology at Carnegie Mellon University in collaboration with Steve Mount at the Center for Bioinformatics and Computational Biology at the University of Maryland, College Park. [Sailfish website]

Running a Sailfish job on Biowulf

The following example uses the sample data that is provided with Sailfish.

Create a batch script along the lines of the one below:

#!/bin/bash
#PBS -N Sailfish

# cd to a directory of your choice
cd /data/username/mydir

# copy the sample data
unzip /usr/local/apps/sailfish/0.5.0/sample_data.zip

# set up the environment
module load sailfish

cd sample_data

# build the index
sailfish index -t transcripts.fasta -o sample_index -k 20 -p 4

# quantify abundance
sailfish quant -i sample_index -o sample_quant -r *.fastq -p 4

Submit this job with:

qsub -l nodes=1 myjob.bat

Documentation
Sailfish documentation