steps used to generate statistics for gabby and laura's data

trim-and-filter.sh

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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