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# 安装RNA-seq数据处理流程
# 代码参考:https://www.jianshu.com/p/a84cd44bac67
# 视频教程见:https://www.bilibili.com/video/av28453557
wget https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
source ~/.bashrc
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
conda config --set show_channel_urls yes
conda create -n rna python=2 #创建名为rna的软件安装环境
source activate rna
conda install -y sra-tools multiqc trim-galore subread hisat2
## 走RNA-seq数据分析流程
dump=/home/jianmingzeng/biosoft/sratoolkit/sratoolkit.2.9.2-centos_linux64/bin/fastq-dump
# 如果使用conda安装的 sra-tools ,那么 fastq-dump命令应该是在环境变量的。
ls ./sra/* | while read id; do ( nohup $dump --gzip --split-3 -O ./ ${id} & ); done ## 批量转换sra到fq格式。
hisat2=/home/jianmingzeng/biosoft/HISAT/hisat2-2.0.4/hisat2
# # 如果使用conda安装的 hisat2,那么 hisat2 命令应该是在环境变量的。
## 索引文件需要自己下载
# https://ccb.jhu.edu/software/hisat2/manual.shtml
# wget ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/data/mm10.tar.gz
index=/home/jianmingzeng/reference/index/hisat/mm10/genome
ls raw_fq/*gz | while read id; do
$hisat2 -p 10 -x $index -U $id -S ${id%%.*}.hisat.sam
done
ls *.sam|while read id ;do (samtools sort -O bam -@ 5 -o $(basename ${id} ".sam").bam ${id});done
rm *.sam
ls *.bam |xargs -i samtools index {}
## gtf文件推荐去gencode数据库下载
gtf=/home/jianmingzeng/reference/gtf/gencode/gencode.vM12.annotation.gtf
featureCounts=/home/jianmingzeng/biosoft/featureCounts/subread-1.5.3-Linux-x86_64/bin/featureCounts
# # # 如果使用conda安装的 subread,那么featureCounts 命令应该是在环境变量的。
$featureCounts -T 5 -p -t exon -g gene_id -a $gtf -o all.id.txt *.bam 1>counts.id.log 2>&1 &
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