#!/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
