Add new file

sortmerna

+###in case of conda enviroment. Check version when first using the software (conda info --envs | grep [NAME SOFTWARE])
+conda activate sortmerna-4.2.0
+
+###Check location databes if migale is not used
+sortmerna -threads 8 -v --reads [FASTQ OR .GZ] --paired_in --aligned FILE_NAME.extendedFrags-rRNA --other FILE_NAME.extendedFrags-mRNA --fastx --ref/usr/local/genome/src/sortmerna-2.0/rRNA_databases/rfam-5s-database-id98.fasta,/projet/mig/work/orue/SORTMERNA_index/index/rfam-5s:/usr/local/genome/src/sortmerna-2.0/rRNA_databases/rfam-5.8s-database-id98.fasta,/projet/mig/work/orue/SORTMERNA_index/index/rfam-5.8s:/usr/local/genome/src/sortmerna-2.0/rRNA_databases/silva-arc-16s-id95.fasta,/projet/mig/work/orue/SORTMERNA_index/index/silva-arc-16s-id95:/usr/local/genome/src/sortmerna-2.0/rRNA_databases/silva-arc-23s-id98.fasta,/projet/mig/work/orue/SORTMERNA_index/index/silva-arc-23s-id98:/usr/local/genome/src/sortmerna-2.0/rRNA_databases/silva-bac-16s-id90.fasta,/projet/mig/work/orue/SORTMERNA_index/index/silva-bac-16s-id90:/usr/local/genome/src/sortmerna-2.0/rRNA_databases/silva-bac-23s-id98.fasta,/projet/mig/work/orue/SORTMERNA_index/index/silva-bac-23s-id98:/usr/local/genome/src/sortmerna-2.0/rRNA_databases/silva-euk-18s-id95.fasta,/projet/mig/work/orue/SORTMERNA_index/index/silva-euk-18s-id95:/usr/local/genome/src/sortmerna-2.0/rRNA_databases/silva-euk-28s-id98.fasta,/projet/mig/work/orue/SORTMERNA_index/index/silva-euk-28s-id98
+
+conda deactivate
+
+