diff --git a/20200821_sort_rRNA_mergeSample.sh b/20200821_sort_rRNA_mergeSample.sh
new file mode 100644
index 0000000..a323a58
--- /dev/null
+++ b/20200821_sort_rRNA_mergeSample.sh
@@ -0,0 +1,64 @@
+conda activate sortmerna_env
+
+export DATABASE=/media/bioinfoteam/SCRATCH_850GB/databases/rna_families
+
+cd /media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/quality_trimming
+
+##################################### on merged sample -> considering as single read ######################################
+
+for filename1 in $(ls *'_merged_qfiltered.fastq')
+
+do
+fileID=`expr match "$filename1" '\([0-9]*C_L1\)_merged'`
+
+
+#echo '**********'
+echo $filename1
+echo $fileID
+
+export OUTFILE1=/media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/rRNA_sorting_merge/${fileID}_aligned
+
+export OUTFILE2=/media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/rRNA_sorting_merge/${fileID}_non_aligned
+
+sortmerna -ref $DATABASE/rfam-5.8s-database-id98.fasta -ref $DATABASE/rfam-5s-database-id98.fasta -ref $DATABASE/silva-arc-16s-id95.fasta -ref $DATABASE/silva-arc-23s-id98.fasta -ref $DATABASE/silva-bac-16s-id90.fasta -ref $DATABASE/silva-bac-23s-id98.fasta -ref $DATABASE/silva-euk-18s-id95.fasta -ref $DATABASE/silva-euk-28s-id98.fasta -reads $filename1 -fastx --aligned $OUTFILE1 --other $OUTFILE2 -paired_in False
+
+rm /home/bioinfoteam/sortmerna/run/kvdb/*
+
+done
+
+
+##################################### on unmerged sample -> considering as paired reads, on separated R1 and R2 ######################################
+
+for filename1 in $(ls *'_R1_unmerged_qfiltered.fastq')
+
+do
+fileID=`expr match "$filename1" '\([0-9]*C_L1\)'`
+
+filename2=$fileID'_R2_unmerged_qfiltered.fastq'
+
+#echo '**********'
+echo $filename1
+echo $fileID
+
+export OUTFILE1=/media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/rRNA_sorting_merge/${fileID}_unmerged_aligned
+
+export OUTFILE2=/media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/rRNA_sorting_merge/${fileID}_unmerged_non_aligned
+
+sortmerna -ref $DATABASE/rfam-5.8s-database-id98.fasta -ref $DATABASE/rfam-5s-database-id98.fasta -ref $DATABASE/silva-arc-16s-id95.fasta -ref $DATABASE/silva-arc-23s-id98.fasta -ref $DATABASE/silva-bac-16s-id90.fasta -ref $DATABASE/silva-bac-23s-id98.fasta -ref $DATABASE/silva-euk-18s-id95.fasta -ref $DATABASE/silva-euk-28s-id98.fasta -reads $filename1 -reads $filename2 -fastx --aligned $OUTFILE1 --other $OUTFILE2 -paired_in True
+
+rm /home/bioinfoteam/sortmerna/run/kvdb/*
+
+done
+
+
+
+
+
+
+
+
+
+
+
+
+