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#!/bin/bash -l
#PBS -N QC_P1-6
#PBS -l walltime=102:00:00
#PBS -l mem=8gb
#PBS -l ncpus=4
#PBS -m bae
#PBS -M email@host
#PBS -j oe


#User-defined parameters:
SAMPLEID=SRR1039513
READ1=SRR1039513_1.fastq
READ2=SRR1039513_2.fastq

#Pipeline:

cd $PBS_O_WORKDIR

#make output folder
mkdir -p trimgalore

# Remove adaptors and poor quality bases/reads using trimgalore. Minimal quality score of 20 (-q20) and minimal length of 50 bases (--length 50)
trim_galore --length 50 --cores 4 --paired -q 20 --fastqc  -o ./trimgalore ${READ1} ${READ2}