Chapter 8 介绍两种下载方法

ascp 注：须conda activate download
prefetch 可省略激活步骤

8.1 ascp

  • 进入NCBI,在DataSets栏下搜索文献测序数据，如bulk码为GSE95424;单细胞码为PRJNA906632;
  • 将BioProject码复制到www.ebi.ac.uk的Enter acsession栏进行搜索;
  • Show Column Selection的fastq_*选项全选中;
  • Download ALL——Generated FASTQ files:FTP,将文件重命名为fq.txt,并上传到服务器。

8.1.1 ENA下载链接改名

sed -i 's/wget -nc ftp:\/\/ftp.sra.ebi.ac.uk/fasp.sra.ebi.ac.uk:/g' fq.txt

8.1.2 运行代码为 nohup ascp.sh >ascp.log 2>&1 &

下载下来的压缩包一般为*.fastq.gz

#!/bin/bash
#ascp.sh 内容如下
#批量下载
cat fq.txt |while read id 
do 
ascp -QT -l 300m -P33001 -k 1 -i ~/.conda/envs/download/etc/asperaweb_id_dsa.openssh era-fasp@$id .
done

#单独下载
ascp -QT -l 300m -P33001 -k 1 -i ~/.conda/envs/download/etc/asperaweb_id_dsa.openssh era-fasp@将①改名后的内容选择一个复制进来 .

8.1.3 将文件转移到raw_data

mkdir raw_data
mv *.fastq.gz raw_data

8.2 prefetch

  • 进入NCBI,在DataSets栏下搜索文献测序数据，如bulk码为GSE95424;单细胞码为PRJNA906632
  • 点击SRA Run Selector进入网页，再点击select选项下的Accession List下载
  • 获得SRR_Acc_List.txt文件，并上传到服务器 注：打开此文件光标要位于空白行的首位。

8.2.1 下载SRR文件

mkdir -p raw_data
#批量下载
nohup prefetch -O ./raw_data --option-file SRR_Acc_List.txt >prefetch.log 2>&1 &

#单独下载一个
prefetch SRRXXXXXXXX

8.2.2 把当前文件夹的下一级子文件夹中的sra文件移动到当前文件夹来

find . -mindepth 2 -maxdepth 2 -type f -name "*.sra" -exec mv {} . \;

8.2.3 将SRA文件转化为fastq文件,完成后删除*.sra文件

#-S是--split-files，#-e 10开十线程，#*.sra所有sra文件 --include-technical为单细胞才加
nohup fasterq-dump -S -e 10 *.sra >faster1.log 2>&1 &


#转化单独一个文件
fasterq-dump -S -e 10 SRRXXXXXXX.sra

8.2.4 将fastq文件压缩为fq.gz文件

#-k 保留原文件，-d是解压
nohup gzip  *.fastq >gzip.log 2>&1 &

#压缩单独一个
gzip SRRXXXXXX.fastq

8.3 R Markdown

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com.

When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

summary(cars)
##      speed           dist       
##  Min.   : 4.0   Min.   :  2.00  
##  1st Qu.:12.0   1st Qu.: 26.00  
##  Median :15.0   Median : 36.00  
##  Mean   :15.4   Mean   : 42.98  
##  3rd Qu.:19.0   3rd Qu.: 56.00  
##  Max.   :25.0   Max.   :120.00

8.4 Including Plots

You can also embed plots, for example:

Note that the echo = FALSE parameter was added to the code chunk to prevent printing of the R code that generated the plot.

Xie, Yihui. 2015. Dynamic Documents with R and Knitr. 2nd ed. Boca Raton, Florida: Chapman; Hall/CRC. http://yihui.org/knitr/.
———. 2024. Bookdown: Authoring Books and Technical Documents with r Markdown. https://github.com/rstudio/bookdown.