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sickle [2017/11/09 21:58] (current)
jokinsey Created sickle documentation
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 +====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.
sickle.txt · Last modified: 2017/11/09 21:58 by jokinsey