Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-10T17:00:29.250Z
Answers.LastActivityDate: 2019-09-12T15:58:08.807Z
Answers.LastEditDate: 2019-09-12T15:58:08.807Z
Answers.UserDisplayName: Mack123456
Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-10T14:50:41.943Z
Answers.Text: what's ENA? and how what would be the right `fastq-dump` command?
Answers.UserDisplayName: 0x90
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-10T14:52:01.787Z
Answers.Text: ENA is the European Nucleotide Archive. Don't use fastq-dump, don't use SRA at all.
Answers.UserDisplayName: Devon Ryan
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-10T14:57:36.660Z
Answers.Text: What would be the equivalent command?
Answers.UserDisplayName: 0x90
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-10T14:58:16.977Z
Answers.Text: wget or curl or just right clicking on the web interface and selecting save.
Answers.UserDisplayName: Devon Ryan
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-10T14:59:01.717Z
Answers.Text: I see, so ENA is a European mirror of GEO?
Answers.UserDisplayName: 0x90
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-10T15:03:07.380Z
Answers.Text: Use aspera, just as with SRA.
Answers.UserDisplayName: Devon Ryan
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-10T16:04:15.097Z
Answers.Text: the link will be here: https://www.ebi.ac.uk/ena/data/view/SRR1658526
Answers.UserDisplayName: StupidWolf
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-10T14:49:17.100Z
Answers.LastActivityDate: 2019-09-10T14:49:17.100Z
Answers.UserDisplayName: Devon Ryan
Body: <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>
  
Tags: <fastq>
Title: Does this FASTQ data contain single or paired end calls?
ThreadText: # 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](https://en.wikipedia.org/wiki/FASTQ_format) 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.
  
  
  ---
  
  