diff --git a/20200717_quality_control_input.sh b/20200717_quality_control_input.sh index 43c8bbf..37d88a2 100644 --- a/20200717_quality_control_input.sh +++ b/20200717_quality_control_input.sh @@ -1,19 +1,19 @@ 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 files ending by .fastq.gz for filename in $(ls *'.fastq.gz') do fastqc $filename done ##based on fastqc.reports of all files: create a summary.html files using multiqc -. multiqc +multiqc .