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Copy pathmerge_F1_F2
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merge_F1_F2
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#!/bin/bash
#SBATCH --job-name=Group1_shortreads_exe
#SBATCH --partition=hpc
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --mem=1g
#SBATCH --time=05:00:00
#SBATCH --output=/shared/Project1_Resources/Group1
#SBATCH --error=/shared/Project1_Resources/Group1
# These steps are required to activate Conda
source $HOME/.bash_profile
conda activate /shared/apps/conda/bio2
mkdir 20230130TM_merge_R1_R2
cat /shared/Project1_Resources/source_data/ds989matt/20211022_045448/Fastq/H164_S1_L00?_R1_001.fastq.gz >> /shared/Project1_Resources/Group1/20230130TM_merge_R1_R2/merged_S1_R1.fq.gz
cat /shared/Project1_Resources/source_data/ds989matt/20211022_045448/Fastq/H3929_S2_L00?_R1_001.fastq.gz >> /shared/Project1_Resources/Group1/20230130TM_merge_R1_R2/merged_S2_R1.fq.gz
cat /shared/Project1_Resources/source_data/ds989matt/20211022_045448/Fastq/H5294_S7_L00?_R1_001.fastq.gz >> /shared/Project1_Resources/Group1/20230130TM_merge_R1_R2/merged_S7_R1.fq.gz
cat /shared/Project1_Resources/source_data/ds989matt/20211022_045448/Fastq/H164_S1_L00?_R2_001.fastq.gz >> /shared/Project1_Resources/Group1/20230130TM_merge_R1_R2/merged_S1_R2.fq.gz
cat /shared/Project1_Resources/source_data/ds989matt/20211022_045448/Fastq/H3929_S2_L00?_R2_001.fastq.gz >> /shared/Project1_Resources/Group1/20230130TM_merge_R1_R2/merged_S2_R2.fq.gz
cat /shared/Project1_Resources/source_data/ds989matt/20211022_045448/Fastq/H5294_S7_L00?_R2_001.fastq.gz >> /shared/Project1_Resources/Group1/20230130TM_merge_R1_R2/merged_S7_R2.fq.gz