Answers.Body: <p>I suggest you follow the advice in <a href="https://bioinformatics.stackexchange.com/users/1628/eric-a-brenner">Eric A Brenner's</a> answer and just download the fastq files. However, if you really really want to use the SRA files for some reason, note that you can use <a href="https://github.com/rvalieris/parallel-fastq-dump" rel="nofollow noreferrer">parallel-fastq-dump</a> to make things faster. Do follow its advice regarding using <code>prefetch</code>.</p>
  
  <p>You'd need to combine that with the answer from <a href="https://bioinformatics.stackexchange.com/users/939/b-nota">b.nota</a> (i.e., put the commands in a <code>for</code> loop).</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-10-17T08:19:27.760Z
Answers.LastActivityDate: 2017-10-17T08:19:27.760Z
Answers.UserDisplayName: Devon Ryan
Answers.Body: <p>Assuming you ultimately just want the fastq files and you know the SRR (run) numbers, I would download them from here: <a href="ftp://ftp.sra.ebi.ac.uk/vol1/fastq/" rel="nofollow noreferrer">ftp://ftp.sra.ebi.ac.uk/vol1/fastq/</a></p>
  
  <p>As for downloading multiple files, I've just used multiple wget commands. I don't know of a way to download all of the files together in like a zipped folder or anything :/</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-10-16T23:35:59.217Z
Answers.LastActivityDate: 2017-10-16T23:35:59.217Z
Answers.UserDisplayName: Eric A Brenner
Answers.Body: <p>This online tool creates download links for the less tech savy:</p>
  <p><a href="https://sra-explorer.info/#" rel="nofollow noreferrer">https://sra-explorer.info/#</a></p>
  <p>Using PRJNA201245 as ID, it provides several codes including a bash script for downloading all files.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-03-21T21:13:48.720Z
Answers.LastActivityDate: 2021-03-21T21:13:48.720Z
Answers.UserDisplayName: Geo Vogler
Answers.Body: <p>Once you <a href="https://github.com/ncbi/sra-tools/wiki/02.-Installing-SRA-Toolkit" rel="nofollow noreferrer">install SRA tools</a>, you can grab a BioProject/SRP accession list (Send to - File - Accession List) and save it to default SRA tools /sra directory, then run (with /sra as cwd):</p>
  <pre><code>prefetch --option-file SraAccList.txt
  cat SraAccList.txt | xargs fasterq-dump --outdir &quot;/your-directory/for-fastq&quot;
  </code></pre>
  <p>P.S. The text file can be any list of accessions, separated by return.
  Tested in Bash</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-03-17T17:46:08.883Z
Answers.LastActivityDate: 2021-04-21T12:14:23.567Z
Answers.LastEditDate: 2021-04-21T12:14:23.567Z
Answers.UserDisplayName: Kostas Pildish
Answers.Body: <p>You can download an entire project using <a href="https://github.com/saketkc/pysradb" rel="nofollow noreferrer">pysradb</a>:</p>
  
  <pre><code>pysradb download -p SRP022054
  </code></pre>
  
  <p>It retains the same schema as SRA.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-24T03:36:28.627Z
Answers.LastActivityDate: 2020-04-24T03:36:28.627Z
Answers.UserDisplayName: Saket Choudhary
Answers.Body: <p>I was able to find a solution for this using <a href="https://www.ncbi.nlm.nih.gov/books/NBK179288/" rel="nofollow noreferrer">Entrez Direct</a> and SRA toolkit :) If you have the project number or <a href="https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP022054" rel="nofollow noreferrer">SRA project number</a>, yours would be SRP022054 in this case for the 36 SRAs, you can use esearch to make a query like so and pipe it into SRA toolkit with this one liner:</p>
  
  <p><code>esearch -db sra -query SRP022054  | efetch --format runinfo | cut -d ',' -f 1 | grep SRR | head -5 | xargs fastq-dump  --skip-technical  --readids --read-filter pass --dumpbase --split-3</code></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-23T22:06:45.480Z
Answers.LastActivityDate: 2020-04-23T22:06:45.480Z
Answers.UserDisplayName: Kai Fung
Answers.Body: <p>A quick look at your link tells me the SRR numbers run from SRR837819 to SRR837856. You can use fastq-dump from the sratoolkit, and make a for loop around it in bash.</p>
  
  <p>Something like this should work:</p>
  
  <pre><code>for (( i = 19; i &lt;= 56; i++ ))
    do
    fastq-dump --accession SRR8378$i
  done
  </code></pre>
  
  <p>After reading <a href="https://bioinformatics.stackexchange.com/users/77/devon-ryan">Devon Ryan</a>'s answer, I realize that you asked for SRA files instead of fastq. This can also be done with prefetch of the sratoolkit:</p>
  
  <pre><code>for (( i = 19; i &lt;= 56; i++ ))
    do
    prefetch SRR8378$i
  done
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-10-17T07:46:10.763Z
Answers.LastActivityDate: 2017-10-17T09:48:28.950Z
Answers.LastEditDate: 2017-10-17T09:48:28.950Z
Answers.UserDisplayName: benn
Body: <p>I want to download all SRA file from the following <a href="https://www.ncbi.nlm.nih.gov/sra?linkname=bioproject_sra_all&amp;from_uid=201245" rel="nofollow noreferrer">project</a>. Is there a method to download all the SRA files at the same time?</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-10-16T21:06:47.150Z
Comments.Text: You could use the R/Bioconductor package [SRAdb](https://www.bioconductor.org/packages/release/bioc/html/SRAdb.html)
Comments.UserDisplayName: John Blischak
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-10-17T10:50:11.887Z
Comments.Text: @JohnBlischak This might be an answer if expanded explaining how SRAdb helps to answer the question
Comments.UserDisplayName: llrs
Tags: <rna-seq><data-download>
Title: Download multiple SRA files
ThreadText: # Download multiple SRA files
  
  (Asked by: username_0 on 2017-10-16)
  
  I want to download all SRA file from the following [project](https://www.ncbi.nlm.nih.gov/sra?linkname=bioproject_sra_all&from_uid=201245). Is there a method to download all the SRA files at the same time?
  
  **Tags:** rna-seq, data-download
  
  > **Comments:**
  > **username_1**: You could use the R/Bioconductor package [SRAdb](https://www.bioconductor.org/packages/release/bioc/html/SRAdb.html)  
  > **username_2**: @username_1 This might be an answer if expanded explaining how SRAdb helps to answer the question  
  
  ---
  
  ## 7 answers
  
  ### Answer by username_9 on 2017-10-17. Score: 5 | Accepted answer
  
  A quick look at your link tells me the SRR numbers run from SRR837819 to SRR837856. You can use fastq-dump from the sratoolkit, and make a for loop around it in bash.
  
  Something like this should work:
  
  ```
  for (( i = 19; i <= 56; i++ ))
    do
    fastq-dump --accession SRR8378$i
  done
  
  ```
  
  After reading [username_3 username_3](https://bioinformatics.stackexchange.com/users/77/username_3-username_3)'s answer, I realize that you asked for SRA files instead of fastq. This can also be done with prefetch of the sratoolkit:
  
  ```
  for (( i = 19; i <= 56; i++ ))
    do
    prefetch SRR8378$i
  done
  
  ```
  
  
  ---
  
  ### Answer by username_3 on 2017-10-17. Score: 3
  
  I suggest you follow the advice in [username_4 A username_4's](https://bioinformatics.stackexchange.com/users/1628/username_4-a-username_4) answer and just download the fastq files. However, if you really really want to use the SRA files for some reason, note that you can use [parallel-fastq-dump](https://github.com/rvalieris/parallel-fastq-dump) to make things faster. Do follow its advice regarding using `prefetch`.
  
  You'd need to combine that with the answer from [b.nota](https://bioinformatics.stackexchange.com/users/939/b-nota) (i.e., put the commands in a `for` loop).
  
  
  ---
  
  ### Answer by username_4 on 2017-10-16. Score: 3
  
  Assuming you ultimately just want the fastq files and you know the SRR (run) numbers, I would download them from here: <ftp://ftp.sra.ebi.ac.uk/vol1/fastq/>
  
  As for downloading multiple files, I've just used multiple wget commands. I don't know of a way to download all of the files together in like a zipped folder or anything :/
  
  
  ---
  
  ### Answer by username_8 on 2020-04-23. Score: 1
  
  I was able to find a solution for this using [Entrez Direct](https://www.ncbi.nlm.nih.gov/books/NBK179288/) and SRA toolkit :) If you have the project number or [SRA project number](https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP022054), yours would be SRP022054 in this case for the 36 SRAs, you can use esearch to make a query like so and pipe it into SRA toolkit with this one liner:
  
  `esearch -db sra -query SRP022054 | efetch --format runinfo | cut -d ',' -f 1 | grep SRR | head -5 | xargs fastq-dump --skip-technical --readids --read-filter pass --dumpbase --split-3`
  
  
  ---
  
  ### Answer by username_5 on 2021-03-21. Score: 0
  
  This online tool creates download links for the less tech savy:
  
  <https://sra-explorer.info/#>
  
  Using PRJNA201245 as ID, it provides several codes including a bash script for downloading all files.
  
  
  ---
  
  ### Answer by username_6 on 2021-03-17. Score: 0
  
  Once you [install SRA tools](https://github.com/ncbi/sra-tools/wiki/02.-Installing-SRA-Toolkit), you can grab a BioProject/SRP accession list (Send to - File - Accession List) and save it to default SRA tools /sra directory, then run (with /sra as cwd):
  
  ```
  prefetch --option-file SraAccList.txt
  cat SraAccList.txt | xargs fasterq-dump --outdir "/your-directory/for-fastq"
  
  ```
  
  P.S. The text file can be any list of accessions, separated by return.
  Tested in Bash
  
  
  ---
  
  ### Answer by username_7 on 2020-04-24. Score: 0
  
  You can download an entire project using [pysradb](https://github.com/saketkc/pysradb):
  
  ```
  pysradb download -p SRP022054
  
  ```
  
  It retains the same schema as SRA.
  
  
  ---
  
  