shell搭建的RNA-seq原始数据处理流程

#!/bin/bash
st=5575800
en=5575805
index=/data/long/RNA-seq/refgenome/bos_tran/Bos_tran
gtf=/data/long/RNA-seq/refgenome/Bos_taurus.UMD3.1.94.gtf
#download SRA data
mkdir 1_SRA
cd 1_SRA
for ((i=$st;i<=$en;i++))
do
wget https://sra-download.ncbi.nlm.nih.gov/srapub/SRR$i
done
cd ..
#convert into fastq
mkdir 2_fastq
cd 2_fastq
export PATH=$PATH:/data/long/biosoft/sratoolkit.2.8.2-1-ubuntu64/bin
for ((i=$st;i<=$en;i++))
do
fastq-dump --split-3 ../1_SRA/SRR$i -O . 
done
cd ..
#fastqc quility control
mkdir 3_fastqc
cd 3_fastqc
for ((i=$st;i<=$en;i++))
do
srr1="../2_fastq/SRR"$i"_1.fastq"
srr2="../2_fastq/SRR"$i"_2.fastq"
fastqc -o . -t 5 -f fastq $srr1
fastqc -o . -t 5 -f fastq $srr2
done
cd ..
#hisat2 
mkdir 4_hisat
cd 4_hisat
#blast
for ((i=$st;i<=$en;i++))
do
hisat2 -p 16 -x $index --sra-acc ../1_SRA/SRR$i -S SRR$i.sam
done
cd ..
#samtools
mkdir 5_samtools
cd 5_samtools
export PATH=$PATH:/data/long/biosoft/samtools-1.6
for ((i=$st;i<=$en;i++))
do
samtools view -bS ../4_hisat/SRR$i.sam > SRR$i.bam
samtools sort SRR$i.bam -o SRR$i.sort.bam
done
cd ..
#stringtie
mkdir 6_stringtie
cd 6_stringtie
export PATH=$PATH:/data/long/biosoft/stringtie-1.3.5.Linux_x86_64
echo "" > mergelist.txt
for ((i=$st;i<=$en;i++))
do
stringtie ../5_samtools/SRR$i.sort.bam -p 4 -G $gtf -o SRR$i.gtf
echo ./SRR$i.gtf >> mergelist.txt
done
stringtie --merge -p 4 -G $gtf -o stringtie_merged.gtf mergelist.txt
for ((i=$st;i<=$en;i++))
do
stringtie -e -B -p 4 -G stringtie_merged.gtf -o ballgown/SRR$i/SRR$i.gtf ../5_samtools/SRR$i.sort.bam
done