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cutadap_batch.srun
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#!/usr/bin/bash
#SBATCH --partition=bgmp ### Partition
#SBATCH --job-name=cutadapt ### Job Name
#SBATCH --output=cutadapt%j ### File in which to store job output
#SBATCH --time=1-00:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --account=bgmp
8_R1 = "/projects/bgmp/shared/2017_sequencing/demultiplexed/8_2F_fox_S7_L008_R1_001.fastq.gz"
8_R2 = "/projects/bgmp/shared/2017_sequencing/demultiplexed/8_2F_fox_S7_L008_R2_001.fastq.gz"
29_R1 = "/projects/bgmp/shared/2017_sequencing/demultiplexed/29_4E_fox_S21_L008_R1_001.fastq.gz"
29_R2 = "/projects/bgmp/shared/2017_sequencing/demultiplexed/29_4E_fox_S21_L008_R2_001.fastq.gz"
ADAPTER_FWD= "AGATCGGAAGAGCACACGTCTGAACTCCAGTCA"
ADAPTER_REV= "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT"
# cutadapt -a ADAPTER_FWD -A ADAPTER_REV -o out.1.fastq -p out.2.fastq reads.1.fastq reads.2.fastq
cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -o 8_2F_fox_S7_L008_R1_001.out.1.fastq -p 8_2F_fox_S7_L008_R2_001.out.2.fastq /projects/bgmp/shared/2017_sequencing/demultiplexed/8_2F_fox_S7_L008_R1_001.fastq.gz /projects/bgmp/shared/2017_sequencing/demultiplexed/8_2F_fox_S7_L008_R2_001.fastq.gz -j 0
cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -o 29_4E_fox_S21_L008_R1_001.out.1.fastq -p 29_4E_fox_S21_L008_R2_001.out.2.fastq /projects/bgmp/shared/2017_sequencing/demultiplexed/29_4E_fox_S21_L008_R1_001.fastq.gz /projects/bgmp/shared/2017_sequencing/demultiplexed/29_4E_fox_S21_L008_R2_001.fastq.gz -j 0