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]
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