metatran_LBE/20200811_sortByName_SamTools.sh
2c0be68cc796master

20200811_sortByName_SamTools.sh
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			conda activate samtools_env

			export WORKING_DIR=/media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/bowtie_output

			cd $WORKING_DIR

			#Sort alignments by name
			for filename in $(ls *'.sam')

			do

			#echo $filename

			fileID=`expr match "$filename" '$[0-9]*C_map_on_d427_hybridAB$'`

			#echo $fileID

			export OUTPUT=/media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/bowtie_output/SAMTools/${fileID}_sort

			samtools sort -o $OUTPUT.sam -n $filename

			done

			#####################################################################################################################

			#Convert SAM into BAM format

			export WORKING_DIR=/media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/bowtie_output/SAMTools

			cd $WORKING_DIR

			for filename in $(ls *'.sam')

			do

			#echo $filename

			samtools view -S -b $filename > $filename.bam

			done