text: user9217: I want to download the following fastq files at the same time in Salmon:
   - SRR10611214
   - SRR10611215
   - SRR10611215
   - SRR10611216
   - SRR10611217
  
  Is there a way to do this using a bash for loop or fastq-dump? or prefetch
  
  user6343: Make a list.txt file containing a single column of SRA numbers to download.
  then:
  for i in $(cat list.txt); do echo $i; date; fasterq-dump -S $i; done
  It works well to use NCBI's web interface to find SRA samples of interest, download and open findings in Excel, then copy single column containing SRA numbers and paste into list.txt using document editor such as vim.
  After downloading including the "R" can be nice:
  for i in *_1.fastq; do mv $i ${i%_1.fastq}_R1.fastq; done
  for i in *_2.fastq; do mv $i ${i%_2.fastq}_R1.fastq; done
  and zip:
  pigz *fastq
  If needed a conda option for downloading fasterq-dump:
  conda install -c bioconda sra-tools
  
  user9212: A sample code is given in the salmon documentation as follows. Source
  #!/bin/bash
  mkdir data
  cd data
  for i in `seq 25 40`; 
  do 
    mkdir DRR0161${i}; 
    cd DRR0161${i}; 
    wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/DRR016/DRR0161${i}/DRR0161${i}_1.fastq.gz; 
    wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/DRR016/DRR0161${i}/DRR0161${i}_2.fastq.gz; 
    cd ..; 
  done
  cd .. 
  
  This could be modified as follows.
  #!/bin/bash
  mkdir data
  cd data
  for i in `seq 14 17`; 
  do 
    wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR106/0${i}/SRR106112${i}/SRR106112${i}_1.fastq.gz; 
    wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR106/0${i}/SRR106112${i}/SRR106112${i}_2.fastq.gz; 
  done
  cd .. 
  
  You can save the code as a shell script and run it from the linux terminal. For example bash download_fastq.sh
  
original_text: 9217: <p>I want to download the following fastq files at the same time in Salmon:</p>
  <pre><code> - SRR10611214
   - SRR10611215
   - SRR10611215
   - SRR10611216
   - SRR10611217
  </code></pre>
  <p>Is there a way to do this using a bash for loop or fastq-dump? or prefetch</p>
   6343: <p>Make a list.txt file containing a single column of SRA numbers to download.</p>
  <p>then:</p>
  <p><code>for i in $(cat list.txt); do echo $i; date; fasterq-dump -S $i; done</code></p>
  <p>It works well to use NCBI's web interface to find SRA samples of interest, download and open findings in Excel, then copy single column containing SRA numbers and paste into list.txt using document editor such as vim.</p>
  <p>After downloading including the &quot;R&quot; can be nice:</p>
  <p><code>for i in *_1.fastq; do mv $i ${i%_1.fastq}_R1.fastq; done</code></p>
  <p><code>for i in *_2.fastq; do mv $i ${i%_2.fastq}_R1.fastq; done</code></p>
  <p>and zip:</p>
  <p><code>pigz *fastq</code></p>
  <p>If needed a conda option for downloading fasterq-dump:</p>
  <p><code>conda install -c bioconda sra-tools</code></p>
   9212: <p>A sample code is given in the salmon documentation as follows. <a href="https://combine-lab.github.io/salmon/getting_started/" rel="nofollow noreferrer">Source</a></p>
  <pre><code>#!/bin/bash
  mkdir data
  cd data
  for i in `seq 25 40`; 
  do 
    mkdir DRR0161${i}; 
    cd DRR0161${i}; 
    wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/DRR016/DRR0161${i}/DRR0161${i}_1.fastq.gz; 
    wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/DRR016/DRR0161${i}/DRR0161${i}_2.fastq.gz; 
    cd ..; 
  done
  cd .. 
  </code></pre>
  <p>This could be modified as follows.</p>
  <pre><code>#!/bin/bash
  mkdir data
  cd data
  for i in `seq 14 17`; 
  do 
    wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR106/0${i}/SRR106112${i}/SRR106112${i}_1.fastq.gz; 
    wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR106/0${i}/SRR106112${i}/SRR106112${i}_2.fastq.gz; 
  done
  cd .. 
  </code></pre>
  <p>You can save the code as a shell script and run it from the linux terminal. For example <code>bash download_fastq.sh</code></p>
  