NCBI-GEO:SRA文件转FASTQ文件

来源

https://www.jianshu.com/p/8322e00a9f8a

https://zhuanlan.zhihu.com/p/353530857

https://github.com/rofl0r/proxychains-ng

通过conda安装纯净环境的sra-tools

  • conda create -n sra_tools -c bioconda sra-tools

  • conda activate sra_tools

  • conda install -c conda-forge pigz -y

  • prefetch

  • wget https://github.com/rofl0r/proxychains-ng/releases/download/v4.16/proxychains-ng-4.16.tar.xz

  • tar -xvf proxychains-ng-4.16.tar.xz

  • cd proxychains-ng-4.16

  • ./configure –prefix=$HOME/dev/proxychains4 –sysconfdir=$HOME/etc

  • make && make install

  • make install-config

  • 添加正确的代理

  • ~/dev/xray/xray -c ~/etc/xui2.json &

  • ~/dev/proxychains4/bin/proxychains4 -f ~/etc/proxychains.conf curl www.github.com

批量下载SRA文件

批量转换为FASTQ文件

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#!/bin/sh
#任务名
TASKN=GSE172205
#设置根目录
ROOTDIR=/home/jovyan/upload/zl_liu/sra/GSE172205
#设置CleanData存放目录
CLEAN=$ROOTDIR/$TASKN

mkdir $CLEAN
for file in `cat SRR_Acc_List.txt`
do
echo $file
mkdir $CLEAN/$file
cd $CLEAN/$file
fasterq-dump --split-3 $ROOTDIR/$file -e 16
pigz -p 16 *
done
  • nano 11.sh
  • chmod +x 11.sh
  • ./11.sh

后续分析

https://occdn.limour.top/1940.html

https://occdn.limour.top/1934.html


NCBI-GEO:SRA文件转FASTQ文件
https://b.limour.top/2025.html
Author
Limour
Posted on
September 24, 2022
Licensed under