RIP-Seq（3）-- 参考基因组比对分析

cat >hisat2.sh
index=/home/zhangyihui/my_data/ref_data/hg38/hisat2_index/grch38/genome
ls ../fq/*.fastq.gz | while read id;
do 
file=$(basename $id)
sample=${file%_*}
hisat2  -p 32 -x $index --no-mixed --no-discordant -1 ../fq/${sample}_1.fastq.gz -2 ../fq/${sample}_2.fastq.gz -S ${sample}.sam >${sample}.log 2>&1 


samtools view -bS ${sample}.sam -o ${sample}.bam 

samtools sort ${sample}.bam -@ 10 -o ${sample}.sorted.bam

rm -rf ${sample}.bam

samtools index -@ 10 ${sample}.sorted.bam

rm -rf  *.sam
multiqc *.log
done
nohup sh hisat2.sh > hisat2.log 2>&1 &

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