metatran_LBE/20200811_count_htseq_withrRNA.sh
b4a73f19d755mapping_withrRNA

20200811_count_htseq_withrRNA.sh
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			conda activate count_env

			export WORKING_DIR=//media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/bowtie_output/SAMTools
			export DATABASE=/media/bioinfoteam/SCRATCH_850GB/databases/annotation_hybridAB/d427AB_annotation_removeFASTA.gff

			cd $WORKING_DIR

			#Count number of reads mapping
			for filename in $(ls *'_withrRNA_sort.sam')

			do

			#echo $filename

			fileID=`expr match "$filename" '$[0-9]*C_map_on_d427_hybridAB_withrRNA_sort$'`

			#echo $fileID

			export OUTPUT=/media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/counting_htseq/${fileID}_samout

			htseq-count -o $OUTPUT -t CDS --nonunique all $filename $DATABASE

			done