metatran_LBE/20200812_count_featuresCount.sh
b4a73f19d755mapping_withrRNA

20200812_count_featuresCount.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.gff
			export OUTPUT=/media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/counting_featuresCount/featureCount.txt

			cd $WORKING_DIR

			#Count number of reads mapping

			featureCounts -p -t CDS -C -O -g ID -a $DATABASE -o $OUTPUT 31C_map_on_d427_hybridAB_sort.bam 32C_map_on_d427_hybridAB_sort.bam 33C_map_on_d427_hybridAB_sort.bam 31C_map_on_d427_hybridAB_withrRNA_sort.bam 32C_map_on_d427_hybridAB_withrRNA_sort.bam 33C_map_on_d427_hybridAB_withrRNA_sort.bam


			#-p If specified, fragments (or templates) will be counted instead of reads. This option is only applicable for paired-end reads
			#-B Only count read pairs that have both ends aligned
			#-C Do not count read pairs that have their two ends mapping to different chromosomes or mapping to same chromosome but on different strands
			#-O Assign reads to all their overlapping meta-features
			#-M Multi-mapping reads will also be counted