===Sickle====

Sickle is a tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. You can find more information on sickle [[https://github.com/najoshi/sickle|here]].

====Environment Setup====

To use Sickle first we need to load the software. The easiest way to do this is to edit your ''.bashrc'' file in your ''$HOME'' directory.

<code>
module load sickle
</code>

In you ''$HOME'' directory create a folder to run sickle jobs and where the test data will be stored.

<code>
razor-l2:jokinsey:~$ mkdir SICKLE-JOBS
razor-l2:jokinsey:~$ cp /share/apps/bioinformatics/sickle-1.33/test/* SICKLE-JOBS/
</code>

====Example Job====

Create a ''PBS'' script names ''sickle.pbs'' with the information below that will be submitted to the queue to run the job.

<code>
#!/bin/bash
#PBS -N sickle
#PBS -q tiny12core
#PBS -j oe
#PBS -o sickle.$PBS_JOBID
#PBS -l nodes=1:ppn=12
#PBS -l walltime=0:05:00

cd $PBS_O_WORKDIR
cp test.fastq /scratch/$PBS_JOBID
cd /scratch/$PBS_JOBID

sickle se -f test.fastq -t illumina -o trimmed_test.fastq

cp trimmed_test.fastq $PBS_O_WORKDIR
</code>

The line that calls sickle is doing a single end trim on the ''test.fastq'' file with the quality setting illumina, and the output file will be trimmed_test.fastq. Sickle also supports paired end trimming and different quality settings, your can find more information [[https://github.com/najoshi/sickle/blob/master/README.md|here]]

All that's left to do is submit the job.

<code>
razor-l2:jokinsey:~/SICKLE-JOBS$ qsub sickle.pbs
</code>

You should see the trimmed out put file ''trimmed_test.fastq'' in the directory you submitted the job from.