#### Specific command
qsub -t 1-8 PBS_viRNA_22nt.sh



qsub -t 1-8 PBS_virus_fenbu.sh

samtools merge -h B10_L1_I343_22.sort.bam sars_total21_23.bam B10_L1_I343_22.sort.bam B12_L1_I345_22.sort.bam B14_L1_I347_22.sort.bam B15_L1_I348_22.sort.bam 

samtools index sars_total21_23.bam

python reads+_.py sars_total21_23.bam 29520 29670

Rscript virus_AUCG+_.R *zheng_AUCG.txt  *fu_AUCG.txt *_virus_AUCG.pdf
### Supplementary Instructions
##The input *.fa file is the reads that are not aligned to the human genome in the sports resultsinput,copy data_sports/output/*/*_fa/*_unmatch_genome.fa to the input folder
##PBS_viRNA_22nt.sh uses bowtie to align to the SARS-COV-2 genome (downloaded by NCBI, remove polyA at the end of the 3'UTR) to obtain the overall bam file and bam files of 21-23nt reads
##The PBS_virus_fenbu.sh script is used to process the bam file that is aligned to the SARS-CoV-2 genome after running PBS_viRNA_22nt.sh to obtain the length distribution on the positive and negative strands
##After running PBS_viRNA_22nt.sh, get the bam file of 21-23nt aligned to the negative strand of the viral genome. Check it in igv, find the site where DCL cleavage may occur (29520-29670), and use reads+_.py to extract the location at this position the positive and negative strands reads of 21-23nt reads, and draw fig4B by hand
#PBS_viRNA_22nt.sh PBS_virus_fenb.sh 需在input文件夹下执行
#Pay attention to the download of R related packages
library(reshape2)
library(ggplot2)
library(ggpubr)
library(viridisLite)
library(viridis)
library(cowplot)

