.sra 格式變?yōu)?.fastq
nohup fastq-dump --split-3 SRR7881539.sra --gzip -O data > log.txt&
hisat2 reads對(duì)比參考基因組
nohup hisat2 -x genome -1 /home/ubuntu/data/data/SRR7881537_1.fastq.gz -2 /home/ubuntu/data/data/SRR7881537_2.fastq.gz -S SRR7881537.sam &
samtools 排序 sam文件轉(zhuǎn)為bam文件 sam文件較大
nohup samtools sort -m 552m SRR7881536.sam -o SRR7881536.bam &
gff文件轉(zhuǎn)化為gtf文件
gffread GCF_001642055.1_Altal1_genomic.gff -T -o tmp.gtf
計(jì)數(shù)
nohup htseq-count -r -f bam /home/ubuntu/data/SRR7881535.bam /home/ubuntu/data/refencegemone/tmp.gtf > SRR7881535.count&
nohup featureCounts -p -t exon -g gene_id -a /home/ubuntu/data/refencegemone/tmp.gtf -o SRR7881536.txt SRR7881536.bam > log.txt
reads提取對(duì)比數(shù)目
awk -F '\t' '{print 7,$8}' OFS='\t' SRR7881536.txt > SRR7881536.out
