<p>The data shown in the fastq files are paired end data.</p>

<p>In fastQ files @ and + do not correspond to R1 and R2.</p>

<p>The <a href="https://en.wikipedia.org/wiki/FASTQ_format" rel="nofollow noreferrer">wikipedia page</a> for fastq files describe the following conventions:</p>

<blockquote>
  <p>A FASTQ file normally uses four lines per sequence.</p>

<pre><code>Line 1 begins with a '@' character and is followed by a sequence identifier and an optional description (like a FASTA title line).
Line 2 is the raw sequence letters.
Line 3 begins with a '+' character and is optionally followed by the same sequence identifier (and any description) again.
Line 4 encodes the quality values for the sequence in Line 2, and must contain the same number of symbols as letters in the sequence.
</code></pre>
</blockquote>

<p><strong>When using fastq-dump
".1" and ".2" stand for read suffices assuming u used the -I flag.</strong></p>

<p>In this case you can see that R1 (".1") and R2 (".2") are within the same file. </p>

CC BY-SA 4.0
2019-09-10T17:00:29.250Z
2019-09-12T15:58:08.807Z
2019-09-12T15:58:08.807Z
Mack123456
<p><a href="https://en.wikipedia.org/wiki/FASTQ_format" rel="nofollow noreferrer">Entries in a fastq file</a> occupy 4 lines each and R1 and R2 are typically in different files. Since that <a href="https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR1658525" rel="nofollow noreferrer">SRA project is 2x51</a> you seem to have run <code>fastq-dump</code> without the <code>--split-3</code> option, so both R1 and R2 are merged together. Make your life easier and never use SRA, but instead just download the individual files from ENA.</p>

CC BY-SA 4.0
2019-09-10T14:50:41.943Z
what's ENA? and how what would be the right `fastq-dump` command?
0x90
CC BY-SA 4.0
2019-09-10T14:52:01.787Z
ENA is the European Nucleotide Archive. Don't use fastq-dump, don't use SRA at all.
Devon Ryan
CC BY-SA 4.0
2019-09-10T14:57:36.660Z
What would be the equivalent command?
0x90
CC BY-SA 4.0
2019-09-10T14:58:16.977Z
wget or curl or just right clicking on the web interface and selecting save.
Devon Ryan
CC BY-SA 4.0
2019-09-10T14:59:01.717Z
I see, so ENA is a European mirror of GEO?
0x90
CC BY-SA 4.0
2019-09-10T15:03:07.380Z
Use aspera, just as with SRA.
Devon Ryan
CC BY-SA 4.0
2019-09-10T16:04:15.097Z
the link will be here: https://www.ebi.ac.uk/ena/data/view/SRR1658526
StupidWolf
CC BY-SA 4.0
2019-09-10T14:49:17.100Z
2019-09-10T14:49:17.100Z
Devon Ryan
<p>I have this fastq data from GEO:</p>

<pre><code>zcat SRR1658526.fastq.gz | head -n 20
@SRR1658526.1 HWI-ST398:296:C1MP4ACXX:1:1101:1093:2094 length=102
GATCTCTATTACTTTTTGAAGGATTNNNNNNNNNNAANTTTTGAATCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNNNN
+SRR1658526.1 HWI-ST398:296:C1MP4ACXX:1:1101:1093:2094 length=102
@&lt;@FFDFDHHFHHIIIIGHBGGGIG##########10#0:BGDDHHII######################################################
@SRR1658526.2 HWI-ST398:296:C1MP4ACXX:1:1101:1167:2107 length=102
ATAATATTGTAGATATAAATGTTATCTAATCTTATCTGATCAGCTTGCTNNATANNNNNNNNNNNNNNNNNNACNTATGNNNNNNNNNNNNNNNNNNNNNCC
+SRR1658526.2 HWI-ST398:296:C1MP4ACXX:1:1101:1167:2107 length=102
CCCFFFFFHHFHHJJIIIIJIJJHJHJJJJIJJIJJJJIJHIJJJJGII#####################################################
</code></pre>

<p>It is supposed to be paired-end sequences. Is the prefix <code>@</code> and <code>+</code> are the R1 and R2? What's the convention here?</p>

<fastq>
Does this FASTQ data contain single or paired end calls?
# Does this FASTQ data contain single or paired end calls?

(Asked by: username_0 on 2019-09-10)

I have this fastq data from GEO:
zcat SRR1658526.fastq.gz | head -n 20
@SRR1658526.1 HWI-ST398:296:C1MP4ACXX:1:1101:1093:2094 length=102
GATCTCTATTACTTTTTGAAGGATTNNNNNNNNNNAANTTTTGAATCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNNNN
+SRR1658526.1 HWI-ST398:296:C1MP4ACXX:1:1101:1093:2094 length=102
@<@FFDFDHHFHHIIIIGHBGGGIG##########10#0:BGDDHHII######################################################
@SRR1658526.2 HWI-ST398:296:C1MP4ACXX:1:1101:1167:2107 length=102
ATAATATTGTAGATATAAATGTTATCTAATCTTATCTGATCAGCTTGCTNNATANNNNNNNNNNNNNNNNNNACNTATGNNNNNNNNNNNNNNNNNNNNNCC
+SRR1658526.2 HWI-ST398:296:C1MP4ACXX:1:1101:1167:2107 length=102
CCCFFFFFHHFHHJJIIIIJIJJHJHJJJJIJJIJJJJIJHIJJJJGII#####################################################

It is supposed to be paired-end sequences. Is the prefix @ and + are the R1 and R2? What's the convention here?

**Tags:** fastq

---

## 2 answers

### Answer by username_2 on 2019-09-10. Score: 4 | Accepted answer

[Entries in a fastq file](https://en.wikipedia.org/wiki/FASTQ_format) occupy 4 lines each and R1 and R2 are typically in different files. Since that [SRA project is 2x51](https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR1658525) you seem to have run `fastq-dump` without the `--split-3` option, so both R1 and R2 are merged together. Make your life easier and never use SRA, but instead just download the individual files from ENA.

> **Comments:**
> **username_0**: what's ENA? and how what would be the right `fastq-dump` command?  
> **username_2**: ENA is the European Nucleotide Archive. Don't use fastq-dump, don't use SRA at all.  
> **username_0**: What would be the equivalent command?  
> **username_2**: wget or curl or just right clicking on the web interface and selecting save.  
> **username_0**: I see, so ENA is a European mirror of GEO?  
> **username_2**: Use aspera, just as with SRA.  
> **username_3**: the link will be here: https://www.ebi.ac.uk/ena/data/view/SRR1658526  

---

### Answer by username_1 on 2019-09-10. Score: 2

The data shown in the fastq files are paired end data.
In fastQ files @ and + do not correspond to R1 and R2.
The wikipedia page for fastq files describe the following conventions:

A FASTQ file normally uses four lines per sequence.
Line 1 begins with a '@' character and is followed by a sequence identifier and an optional description (like a FASTA title line).
Line 2 is the raw sequence letters.
Line 3 begins with a '+' character and is optionally followed by the same sequence identifier (and any description) again.
Line 4 encodes the quality values for the sequence in Line 2, and must contain the same number of symbols as letters in the sequence.


When using fastq-dump
".1" and ".2" stand for read suffices assuming u used the -I flag.
In this case you can see that R1 (".1") and R2 (".2") are within the same file.


---

