Table of Contents

Bowtie2

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. You can find more information about Bowtie2 here.

Enviornment and Setup

First we we must load the bowtie2 module. The easiest way to do the is to add it to your .bashrc file, by including its load command. 

module load bowtie2

In your home directory add a location to store the files to process in the example. 

razor-l3:jokinsey:~$ mkdir BOWTIE-JOBS

Navigate into the directory and copy the necessary files from the examples in the bowtie2 application. 

azor-l3:jokinsey:~$ cd BOWTIE-JOBS/
razor-l3:jokinsey:~/BOWTIE-JOBS$ cp /share/apps/bowtie2/bowtie2-2.2.3/example/reference/lambda_virus.fa .
razor-l3:jokinsey:~/BOWTIE-JOBS$ cp /share/apps/bowtie2/bowtie2-2.2.3/example/reads/reads_1.fq .

Example Job

Create a PBS script in your $HOME/BOWTIE-JOBS/ directory to run the example that has all of the information listed below. 

#!/bin/bash
#PBS -q tiny12core
#PBS -N bowtie2
#PBS -l nodes=1:ppn=12
#PBS -j oe
#PBS -m abe
#PBS -M jokinsey@uark.edu
#PBS -l walltime=00:05:00

cd $PBS_O_WORKDIR
cp lambda_virus.fa /scratch/$PBS_JOBID
cp reads_1.fq /scratch/$PBS_JOBID
cd /scratch/$PBS_JOBID

bowtie2-build lambda_virus.fa lambda_virus
bowtie2 -x lambda_virus -U reads_1.fq -S eg1.sam

mv lambda_virus* eg1.sam $PBS_O_WORKDIR/

The PBS script above copies the unindexed FASTA file for the lambda virus and the FASTAQ file containing the unpaired reads for the lambda phage to the /scratch/$PBS_JOBID directory where we will run the computation.

The bowtie2-build line will output files that represent the index for the Lambda phage reference genome. The line below that runs the bowtie2 aligner, and outputs the alginments to a SAM file called eg1.sam. Then the output lambdavirus index files and the alignment results stored in the eg1.sam file, are moved to the $PBS_O_WORKDIR directory where the job was submitted from. Submit the job to the queue. <code> razor-l3:jokinsey:~/BOWTIE-JOBS$ qsub bowtie2.pbs </code> More information on how to interpret a SAM file can be found here