metatran_LBE/20200814_quality_control_rRNAsort.sh
2c0be68cc796master

20200814_quality_control_rRNAsort.sh
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			conda activate multiqc_env

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

			#Quality Control

			##quality check on all files after SortMeRNA on non-aligned sequences
			for filename in $(ls *'non_aligned.fastq')

			do

			fastqc $filename
			done

			#integrate fastqc reports
			multiqc .