sortmerna分析rRNA含量

sortmerna分析双端数据的时候需要用自带的脚本将read1和read2合并为一个fastq

for ((x=1;x<=20;x++)); do sh /media/shen/disk3/biosoft/sortmerna-2.1b/scripts/merge-paired-reads.sh $x.R1.paired.fastq $x.R2.paired.fastq sortmerna-merge/merge.$x.fastq; done

for ((x=2;x<=17;x++)); do ./../sortmerna --ref rfam-5.8s-database-id98.fasta,rfam-5.8s-database-id98.idx:rfam-5s-database-id98.fasta,rfam-5s-database-id98.idx:silva-arc-16s-id95.fasta,silva-arc-16s-id95.idx:silva-arc-23s-id98.fasta,silva-arc-23s-id98.idx:silva-bac-16s-id90.fasta,silva-bac-16s-id90.idx:silva-bac-23s-id98.fasta,silva-bac-23s-id98.idx:silva-euk-18s-id95.fasta,silva-euk-18s-id95.idx:silva-euk-28s-id98.fasta,silva-euk-28s-id98.idx --reads ../scripts/Br_RNA.$x.fastq --aligned $x.out -a 40 -m 61440 --log ; done

multiqc将结果log文件合并

multiqc .