安装miniconda

wget -c https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh Miniconda3-latest-Linux-x86_64.sh
source ~/.bashrc

安装相关软件

###安装aspera加速下载
conda install -c hcc aspera-cli -y
###安装samtools
conda install -c bioconda samtools openssl=1.0 -y
###安装sratoolkit hisat2 stringtie
conda install -c bioconda sra-tools hisat2 stringtie -y
###下载trimmomatic并解压
wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.39.zip
unzip Trimmomatic-0.39.zip

注：如果调用samtools出现如下报错：samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
问题出在openssl的版本，通过conda install openssl=1.0 -y 来确保安装openssl的1.0.2版本

下载sra数据并转换成fastq

使用prefetch命令进行下载，命令形如prefetch SRRXXXXXX SRRXXXXX。
下载完成后，可以用tree来查看下载结果。
使用fasterq-dump将sra文件转换成fastq：

fasterq-dump -e 60 -S *.sra

转录组定量

所有sra数据进行trimmomatic修剪

双端PE

for i in *.sra
do
java -jar /data/software/Trimmomatic-0.39/trimmomatic-0.39.jar PE -threads 60 ${i}_1.fastq ${i}_2.fastq ${i}_clean_1.fastq ${i}_unpaired_1.fastq ${i}_clean_2.fastq ${i}_unpaired_2.fastq ILLUMINACLIP:/data/software/Trimmomatic-0.39/adapters/TruSeq3-PE.fa:2:30:10:2:keepBothReads LEADING:3 TRAILING:3 MINLEN:36
done

单端SE

for i in *.sra
do
java -jar /data/software/Trimmomatic-0.39/trimmomatic-0.39.jar SE -threads 60 ${i}.fastq  ${i}_clean.fastq ILLUMINACLIP:/data/software/Trimmomatic-0.39/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
done

Hisat2+stringtie代码举例

构建索引Index

hisat2-build Ghirsutum_527_v2.0.fa genome

双端PE

ref=Ghirsutum_527_v2.0.fa
gff=Ghirsutum_527_v2.1.gene.gff3
index=genome
label=Ghir
out=SRR5178068
fq1="SRR5178068.sra_clean_1.fastq,SRR5186513.sra_clean_1.fastq"
fq2="SRR5178068.sra_clean_2.fastq,SRR5186513.sra_clean_2.fastq"
hisat2 --dta -p 60 -1 ${fq1} -2 ${fq2} -x ${index} -S ${out}.sam
samtools view -@ 60 -b -S ${out}.sam > ${out}.bam
samtools sort -@ 60 -m 4G -o ${out}.sorted.bam ${out}.bam
stringtie -p 60 -G ${gff} -B -e -l ${label} -o ${out}/${out}.gtf ${out}.sorted.bam

单端SE

ref=G.arboreum_BGI-A2_assembly.fa
gff=G.arboreum_BGI-A2_v1.0_transcripts.gff3
index=genome
label=Garb
out=SRR617065
fq="SRR617065.sra_clean.fastq,SRR617067.sra_clean.fastq"
hisat2 --dta -p 60 -U ${fq} -x ${index} -S ${out}.sam
samtools view -@ 60 -b -S ${out}.sam > ${out}.bam
samtools sort -@ 60 -m 4G -o ${out}.sorted.bam ${out}.bam
stringtie -p 60 -G ${gff} -B -e -l ${label} -o ${out}/${out}.gtf ${out}.sorted.bam注

注：最后输出文件包含我想要的表达量gtf文件（包括FPKM,TPM）以及几个.ctab中间文件。我用了60个线程，注意修改代码中的线程数。