metatran_LBE/20200821_Separate_R1_R2.sh
f7a1ec8cb8efmaster

20200821_Separate_R1_R2.sh
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			cd /media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/merge

			for filename in $(ls *'_unmerged.fastq')

			do
			fileID=`expr match "$filename" '$[0-9]*C_L1$'`

			#echo '**********'
			echo $fileID
			echo $filename

			paste - - - - - - - - < $filename \
			\| tee >(cut -f 1-4 \| tr "\t" "\n" > ${fileID}_R1_unmerged.fastq ) \
			\| cut -f 5-8 \| tr "\t" "\n" > ${fileID}_R2_unmerged.fastq

			done