metatran_LBE/20200717_quality_control.sh
2e37c25fc5f2master

20200717_quality_control.sh
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			conda activate multiqc_env

			export WORKING_DIR=/media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic
			cd $WORKING_DIR

			#Quality Control
			##quality check on specific files
			fastqc 31C_L1_R1_001_7JbTlroBLabe.fastq.gz 31C_L1_R2_001_yDmE80VNE4Et.fastq.gz 32C_L1_R1_001_wtOj7xHt2Rwh.fastq.gz 32C_L1_R2_001_wLqzFGxMmzNn.fastq.gz

			##quality check on all fies ending by .fastq.gz
			for filename in $(ls *'.fastq.gz')

			do

			fastqc $filename
			done