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 here.
To use Sickle first we need to load the software. The easiest way to do this is to edit your
.bashrc file in your
module load sickle
$HOME directory create a folder to run sickle jobs and where the test data will be stored.
razor-l2:jokinsey:~$ mkdir SICKLE-JOBS razor-l2:jokinsey:~$ cp /share/apps/bioinformatics/sickle-1.33/test/* SICKLE-JOBS/
PBS script names
sickle.pbs with the information below that will be submitted to the queue to run the job.
#!/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 $PBS_O_WORKDIR
The line that calls sickle is doing a single end trim on the
test.fastq file with the quality setting illumina, and the output file will be trimmed_test.fastq. Sickle also supports paired end trimming and different quality settings, your can find more information here
All that's left to do is submit the job.
razor-l2:jokinsey:~/SICKLE-JOBS$ qsub sickle.pbs
You should see the trimmed out put file
trimmed_test.fastq in the directory you submitted the job from.