单端测序文件

for i in *IP*fastq; do

 ~/Software/sortmerna-2.1b/sortmerna --ref /home/zhou/Software/sortmerna-2.1b/index/human_rRNA.fa,/home/zhou/Software/sortmerna-2.1b/index/human_rRNA_db: --reads $i --num_alignments 1 --fastx --aligned reads_rRNA --other ${i}_rmrRNA.fq --log -a 8 -m 24000 -v;

 done

双端测序

合并read files

/path_to_sortmerna/scripts/merge-paired-reads.sh reads_1.fq reads_2.fq reads_interleaved.fq

去除rRNA

 ~/Software/sortmerna-2.1b/sortmerna --ref /home/zhou/Software/sortmerna-2.1b/index/human_rRNA.fa,/home/zhou/Software/sortmerna-2.1b/index/human_rRNA_db: --reads $i --num_alignments 1 --fastx --aligned reads_rRNA --other ${i}_rmrRNA.fq --log -a 8 -m 24000 --paired_in -v;

分解merged的read flie

/path_to_sortmerna/scripts/unmerge-paired-reads.sh reads_non_rRNA.fq reads_non_rRNA_1.fq reads_non_rRNA_2.fq