Answers.Body: <p>When I was trying to upload MinION data to SRA, they wouldn't allow me to upload only the raw signal data (i.e. FAST5 files). Every file needed to contain a FASTQ sequence, and this sequence was extracted from the file and stored in the archive. Given this, I don't expect it will be possible to retrieve signal or event information from SRA. I also don't expect this will be possible in the future either, given that the SRA database expects every record to have a FASTQ-like sequence attached.</p>
  
  <p>However, EBI/ENA <em>do</em> allow the upload of raw FAST5 files to the database (e.g. <a href="https://www.ebi.ac.uk/ena/data/view/PRJEB20824" rel="nofollow noreferrer">here</a>), but there are no FAST5 reads for the specific single-cell B1a study you have indicated. If you're interested specifically in that study, then I recommend that you ask Miten Jain directly for access to those reads; he should have another method to give you access to them.</p>
  
  <p>ENA is "ready" for ONT reads, but researchers need to upload their reads to ENA in order for that database to be useful.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-11-27T17:31:07.010Z
Answers.Text: Thanks for sharing that, I guess SRA and ENA are not completely ready yet for ONT.
Answers.UserDisplayName: benn
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Answers.LastEditDate: 2017-11-27T18:02:06.110Z
Answers.UserDisplayName: gringer
Answers.Body: <p>I would suggest trying an alternative way, as the FAST5 is a fairly new entry in SRA - 6 public datasets as of <a href="https://www.ncbi.nlm.nih.gov/sra/?term=fast5" rel="nofollow noreferrer">today</a>. </p>
  
  <p>You can search the ERX/ERR entry you got from SRA in <a href="https://www.ebi.ac.uk/ena" rel="nofollow noreferrer">ENA</a> and either (1) direct download it via ftp or (2) redirect to Galaxy. </p>
  
  <p>Here's a <a href="https://www.bioconductor.org/packages/devel/data/experiment/vignettes/minionSummaryData/inst/doc/creating-Styphi-Dataset.html" rel="nofollow noreferrer">tutorial</a> that might be interesting for you: basically, you first get the archive from ENA, then find the FAST5 files in the top level of the downloaded archive, all to be processed in R using <code>Fast5Summary</code> objects from <a href="https://www.bioconductor.org/packages/devel/bioc/vignettes/IONiseR/inst/doc/IONiseR.html" rel="nofollow noreferrer">IONiseR</a> package.</p>
  
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Answers.Text: Thanks, great idea! However, on [ENA](https://www.ebi.ac.uk/ena/data/search?query=SRR5286963) I can only download fastq or the SRA file or am I missing something?
Answers.UserDisplayName: benn
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Answers.Text: I guess there are no fast5 associated with `SRR5286963` (simple filtered search), so maybe the easiest solution would be to directly ask the publishers - there is possibility that they just uploaded the fastq (e.g. from poretools extraction) instead of the fast5, because of the archive size.
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Answers.UserDisplayName: aechchiki
Body: <p>I found some Nanopore MinION data on SRA, which I would like to investigate. I use <code>sratoolkit</code> for Illumina data all the time, but I am not sure how to get the <code>fast5</code> file from the <code>sra</code> file.</p>
  
  <p>What I have tried is to <code>prefecth</code> it, but then I don't know which command to use for <code>.sra</code> to <code>.fast5</code> conversion. Not with fastq-dump, I assume?</p>
  
  <pre><code>prefetch -v SRR5286963 --max-size 50000000
  </code></pre>
  
Tags: <nanopore><fast5><sratoolkit>
Title: How to get Nanopore MinION fast5 from SRA
ThreadText: # How to get Nanopore MinION fast5 from SRA
  
  (Asked by: username_0 on 2017-11-27)
  
  I found some Nanopore MinION data on SRA, which I would like to investigate. I use `sratoolkit` for Illumina data all the time, but I am not sure how to get the `fast5` file from the `sra` file.
  
  What I have tried is to `prefecth` it, but then I don't know which command to use for `.sra` to `.fast5` conversion. Not with fastq-dump, I assume?
  
  ```
  prefetch -v SRR5286963 --max-size 50000000
  
  ```
  
  **Tags:** nanopore, fast5, sratoolkit
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_1 on 2017-11-27. Score: 3
  
  When I was trying to upload MinION data to SRA, they wouldn't allow me to upload only the raw signal data (i.e. FAST5 files). Every file needed to contain a FASTQ sequence, and this sequence was extracted from the file and stored in the archive. Given this, I don't expect it will be possible to retrieve signal or event information from SRA. I also don't expect this will be possible in the future either, given that the SRA database expects every record to have a FASTQ-like sequence attached.
  
  However, EBI/ENA *do* allow the upload of raw FAST5 files to the database (e.g. [here](https://www.ebi.ac.uk/ena/data/view/PRJEB20824)), but there are no FAST5 reads for the specific single-cell B1a study you have indicated. If you're interested specifically in that study, then I recommend that you ask Miten Jain directly for access to those reads; he should have another method to give you access to them.
  
  ENA is "ready" for ONT reads, but researchers need to upload their reads to ENA in order for that database to be useful.
  
  > **Comments:**
  > **username_0**: Thanks for sharing that, I guess SRA and ENA are not completely ready yet for ONT.  
  
  ---
  
  ### Answer by username_2 on 2017-11-27. Score: 2
  
  I would suggest trying an alternative way, as the FAST5 is a fairly new entry in SRA - 6 public datasets as of [today](https://www.ncbi.nlm.nih.gov/sra/?term=fast5).
  
  You can search the ERX/ERR entry you got from SRA in [ENA](https://www.ebi.ac.uk/ena) and either (1) direct download it via ftp or (2) redirect to Galaxy.
  
  Here's a [tutorial](https://www.bioconductor.org/packages/devel/data/experiment/vignettes/minionSummaryData/inst/doc/creating-Styphi-Dataset.html) that might be interesting for you: basically, you first get the archive from ENA, then find the FAST5 files in the top level of the downloaded archive, all to be processed in R using `Fast5Summary` objects from [IONiseR](https://www.bioconductor.org/packages/devel/bioc/vignettes/IONiseR/inst/doc/IONiseR.html) package.
  
  > **Comments:**
  > **username_0**: Thanks, great idea! However, on [ENA](https://www.ebi.ac.uk/ena/data/search?query=SRR5286963) I can only download fastq or the SRA file or am I missing something?  
  > **username_2**: I guess there are no fast5 associated with `SRR5286963` (simple filtered search), so maybe the easiest solution would be to directly ask the publishers - there is possibility that they just uploaded the fastq (e.g. from poretools extraction) instead of the fast5, because of the archive size.  
  
  ---
  
  