<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>

CC BY-SA 4.0
2021-05-05T16:10:43.943Z
2021-05-05T16:10:43.943Z
winni2k
<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>

CC BY-SA 4.0
2021-05-06T06:54:25.407Z
Regarding the follow-up question: SRA files are a red herring. Nobody I know cares about the SRA file format ¯\\_(ツ)_/¯
winni2k
<rna-seq>
Base abbreviations other than ACTGU in sequence file
# 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 spots
looking at them I expected to see ACGU (this was meant to be an RNA sequence), but what I see are like

AAFFFJJJFJJJJJJJJJJJJJJJJJJJJJFJJF

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]
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>


---

