Answers.Body: <p>I usually convert SRA files to FASTQ before doing any further processing, but the tooling for converting SRA files is cumbersome.</p>
  <p>To simplify things, I recommend you download the FASTQ file directly. The ENA currently has a nicer interface for doing these things. Here is a link to download the FASTQ files for the SRA sequencing run associated with the SRA experiment you are describing: <a href="https://www.ebi.ac.uk/ena/browser/view/SRR11588968" rel="nofollow noreferrer">https://www.ebi.ac.uk/ena/browser/view/SRR11588968</a></p>
  <p>A description of the FASTQ format can be found here: <a href="https://en.wikipedia.org/wiki/FASTQ_format" rel="nofollow noreferrer">https://en.wikipedia.org/wiki/FASTQ_format</a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-05-05T16:10:43.943Z
Answers.LastActivityDate: 2021-05-05T16:10:43.943Z
Answers.UserDisplayName: winni2k
Body: <p><strong>Short question:</strong><br />
  where can I find what <code>F</code> and <code>J</code> and <code>&lt;</code> and <code>-</code> and <code>7</code> mean in a Sequence file?</p>
  <p><strong>Longer version:</strong><br />
  I was looking at this sequence file I got from NCBI (it's an sra file? if that is the correct terminology) and I used the <code>sratoolkit</code> to print out a few <code>spot</code>s</p>
  <p>looking at them I expected to see ACGU (this was meant to be an RNA sequence), but what I see are like</p>
  <blockquote>
  <p>AAFFFJJJFJJJJJJJJJJJJJJJJJJJJJFJJF&lt;JJ77AJJJJ-JJJJJFF7FA--F7FAJJ7&lt;AJ-FJA&lt;J&lt;JJFA&lt;&lt;77F-JJJJJJF&lt;JF&lt;7-FF-A-----A-77JJ7FJJF-FFFAJ&lt;&lt;-FJJFAJAFFAFFFFF&lt;7A7JFJJ7AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJFJJJJJJJJJJJJAA&lt;JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJAAFFJJFJJJJJJJJJJJJJJFJ-FJF</p>
  </blockquote>
  <p>Where can I find a reference to help me &quot;understand&quot; this?<br />
  I mean I assume <code>-</code> means missed or unknown? or is it meant to be already aligned and these are deletions?</p>
  <p>I appreciate any pointer to get started. as you must have observed I am a total noob.</p>
  <p>I got the file from: <a href="https://www.ncbi.nlm.nih.gov/sra/SRX8156420%5Baccn%5D" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/sra/SRX8156420[accn]</a></p>
  <p>Then I did a</p>
  <pre><code> ./fastq-dump -X 5 -Z ERR4557575
  
  </code></pre>
  <p>Follow-up question:</p>
  <ul>
  <li>Where do you look for the quality scores ranges and such, I guess as @winnie2k suggested I should convert this to FASTQ and make my life easier, but still wanted to understand the file better.</li>
  </ul>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-05-06T06:54:25.407Z
Comments.Text: Regarding the follow-up question: SRA files are a red herring. Nobody I know cares about the SRA file format ¯\\_(ツ)_/¯
Comments.UserDisplayName: winni2k
Tags: <rna-seq>
Title: Base abbreviations other than ACTGU in sequence file
ThreadText: # Base abbreviations other than ACTGU in sequence file
  
  (Asked by: username_0 on 2021-05-05)
  
  **Short question:**  
  where can I find what `F` and `J` and `<` and `-` and `7` mean in a Sequence file?
  
  **Longer version:**  
  I was looking at this sequence file I got from NCBI (it's an sra file? if that is the correct terminology) and I used the `sratoolkit` to print out a few `spot`s
  
  looking at them I expected to see ACGU (this was meant to be an RNA sequence), but what I see are like
  
  > AAFFFJJJFJJJJJJJJJJJJJJJJJJJJJFJJF<JJ77AJJJJ-JJJJJFF7FA--F7FAJJ7<AJ-FJA<J<JJFA<<77F-JJJJJJF<JF<7-FF-A-----A-77JJ7FJJF-FFFAJ<<-FJJFAJAFFAFFFFF<7A7JFJJ7AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJFJJJJJJJJJJJJAA<JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJAAFFJJFJJJJJJJJJJJJJJFJ-FJF
  
  Where can I find a reference to help me "understand" this?  
  I mean I assume `-` means missed or unknown? or is it meant to be already aligned and these are deletions?
  
  I appreciate any pointer to get started. as you must have observed I am a total noob.
  
  I got the file from: [https://www.ncbi.nlm.nih.gov/sra/SRX8156420[accn]](https://www.ncbi.nlm.nih.gov/sra/SRX8156420%5Baccn%5D)
  
  Then I did a
  
  ```
   ./fastq-dump -X 5 -Z ERR4557575
  
  ```
  
  Follow-up question:
  
  * Where do you look for the quality scores ranges and such, I guess as @winnie2k suggested I should convert this to FASTQ and make my life easier, but still wanted to understand the file better.
  
  **Tags:** rna-seq
  
  > **Comments:**
  > **username_1**: Regarding the follow-up question: SRA files are a red herring. Nobody I know cares about the SRA file format ¯\\_(ツ)_/¯  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2021-05-05. Score: 3 | Accepted answer
  
  I usually convert SRA files to FASTQ before doing any further processing, but the tooling for converting SRA files is cumbersome.
  
  To simplify things, I recommend you download the FASTQ file directly. The ENA currently has a nicer interface for doing these things. Here is a link to download the FASTQ files for the SRA sequencing run associated with the SRA experiment you are describing: <https://www.ebi.ac.uk/ena/browser/view/SRR11588968>
  
  A description of the FASTQ format can be found here: <https://en.wikipedia.org/wiki/FASTQ_format>
  
  
  ---
  
  