====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 [[http://bowtie-bio.sourceforge.net/bowtie2/index.shtml|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.

<code>
module load bowtie2
</code>

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

<code>
razor-l3:jokinsey:~$ mkdir BOWTIE-JOBS
</code>

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

<code>
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 .
</code>

====Example Job====

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

<code>
#!/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/
</code>

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 lambda_virus 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 [[http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#sam-output|here]]