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twaddlac/trim-and-filter.sh

Created May 25, 2017 16:09
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steps used to generate statistics for gabby and laura's data
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trim-and-filter.sh
�
module load trimmomatic
cd /scratch/at120/gabby-laura-stats/
# for i in $(ls *fastq | perl -pe 's/\.fastq//g'); do mv $i.fastq $(echo $i | perl -pe 's/^C.+l0(\d)n0(\d)_(.+)\.3.+/$3_l$1.r$2.fastq/g'); done
java -jar /share/apps/trimmomatic/0.36/trimmomatic-0.36.jar PE -threads 12 $fastq.r1.fastq $fastq.r2.fastq -baseout $fastq.fastq ILLUMINACLIP:adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
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