Answers.Body: <p>Fasterq comes from the latest version of sratools. So if you check the <a href="https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump" rel="nofollow noreferrer">manual</a> , it says the equivalence is:</p>
  <blockquote>
  <p>fastq-dump SRRXXXXXX --split-3 --skip-technical</p>
  <p>fasterq-dump SRRXXXXXX</p>
  </blockquote>
  <p>In older versions of sratoolkit, if you use fastq-dump without specifying --split-3 for paired-end reads, you get the format mentioned, spotID.1 for forward, spotID.2 for reverse:</p>
  <pre><code>fastq-dump SRR6462984.sra
  more SRR6462984.fastq
  </code></pre>
  <p>You get:</p>
  <pre><code>@SRR6462984.1 1 length=301
  NATCTGCCCGTTCCACATAAACACCGTTAAACATCGATAGAGCGAAATAAAGCTGCTGAGTGATGTGATGATAAAGCTTTTCCGTTCTGACACGATCTTCCATCTCGTCTATCATTGCATCGAGAGCGTCAGAGATCGCAAGCAGTGCGGATATTGCCGTCCGTCTTGAAGCTTTGGCAGAGCCAGGCGGAATTTGTTTATCGGATAGTGTTTATGCGCAAATTTAGCATATGATTTCCGACAACTTTTGCTTCATCGGGCCGCAAAGCGTGAAAAACAGTGTCGTCACCGTTGATGTGTG
  +SRR6462984.1 1 length=301
  #/AAAEE/EEEA/EAAEEAEE/EE/EEA/EEEEE/AAE/EE/EAEAE//EEAEE/EEEEE&lt;EEEEE/EE&lt;EE/AEEEE/EAEEEEA/E&lt;EEAEAEEEEEEAEEEE&lt;EEAEEEEEAAAEEE/EEEEE/E//AEEEE6EA66EE&lt;&lt;&lt;EAAA/AAAAAE/E6E/EA/AE/AEEEEEEAAEEEEA6EEEEEEEEE/EEE/AEEAAAEEEAE/E/EEEEEA//E//EEE/EEE/A&lt;//AE/EE//6A///AA/E//E/E/EE//AE//AAEEE////E/A&lt;AAE/EEAE//A//6/A&lt;/&lt;6/&lt;/E/
  @SRR6462984.2 2 length=302
  NTCAGCAGGCGCCGTAACTTCAGCAAAACTGTAGCTATAACTTTTCCGAACTTTATACCTAACTTCGCTTTCCTAGCACTGTATAAAATGCCTAAAAGAAATCAGCAGGCGCCGTCACTTCAAAAAATCAGTATGGATCAATCAGACGCGGAGCTTATTAAAACAGAGCTTATTAAAAATTATGTCTTTCTTCTTCTTTCAGCAATTCGCAACGTAAAATTCAAAATTTTGGACGCCGTAATTGCGCAGGAACCAATTCAAAGAGGCGGCGGCCAATTAATTCCAACGTCTCGAAGAGTGGC
  +SRR6462984.2 2 length=302
  </code></pre>
  <p>With the latest version, it by defaults splits the paired end sra file into forward and reverse fastq (i.e --split-3):</p>
  <pre><code>fasterq-dump SRR6462984.sra 
  head -2 SRR6462984_*.fastq
  </code></pre>
  <p>And you get</p>
  <pre><code>==&gt; SRR6462984_1.fastq &lt;==
  @SRR6462984.1 1 length=150
  NATCTGCCCGTTCCACATAAACACCGTTAAACATCGATAGAGCGAAATAAAGCTGCTGAGTGATGTGATGATAAAGCTTTTCCGTTCTGACACGATCTTCCATCTCGTCTATCATTGCATCGAGAGCGTCAGAGATCGCAAGCAGTGCGG
  
  ==&gt; SRR6462984_2.fastq &lt;==
  @SRR6462984.1 1 length=151
  ATATTGCCGTCCGTCTTGAAGCTTTGGCAGAGCCAGGCGGAATTTGTTTATCGGATAGTGTTTATGCGCAAATTTAGCATATGATTTCCGACAACTTTTGCTTCATCGGGCCGCAAAGCGTGAAAAACAGTGTCGTCACCGTTGATGTGTG
  </code></pre>
  <p>So if you need to get back the .1 and .2 format, use fastq-dump from the latest installation.</p>
  <p>I would suggest sticking to the newest format, with 2 files, because fastq-dump will be deprecated in the future.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-08-09T03:37:05.800Z
Answers.Text: Can you have a look at this https://bioinformatics.stackexchange.com/questions/21407/multiple-srr-id-downloaded-for-single-gsm-ids-input-issue
Answers.UserDisplayName: PesKchan
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-10-24T14:26:48.720Z
Answers.LastActivityDate: 2019-10-24T14:26:48.720Z
Answers.LastEditDate: 2020-06-18T08:30:41.743Z
Answers.UserDisplayName: StupidWolf
Body: <p>After using files that I downloaded from the SRA with fasterq-dump, I realize I am not 100% sure that I have all the data.</p>
  
  <p>I noticed in my downstream analysis that I seem to be missing the .1 and .2 numbers in the code associated with individual reads with the same spot ID. Then I noticed that my initial fastq file doesn't seem to have those either.</p>
  
  <p>So I'm wondering if the -split-spot option that I used is doing what I want it do do, which is 'get all the sequence data', and how does it differ from --concatenate-reads. I am afraid I did not understand this from the program description. Please help?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-10-24T11:35:30.207Z
Comments.Text: Hi Laura, do you have paired-end reads? Can you provide the SRA accession too?
Comments.UserDisplayName: StupidWolf
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-10-24T13:05:47.350Z
Comments.Text: @StupidWolf It looks like they're paired. Eg. SRR6462984.63.1 and SRR6462984.63.2 .
Comments.UserDisplayName: Laura
Tags: <fastq><sratoolkit>
Title: Fasterq-dump: --split-spot or -concatenate-reads?
ThreadText: # Fasterq-dump: --split-spot or -concatenate-reads?
  
  (Asked by: username_0 on 2019-10-24)
  
  After using files that I downloaded from the SRA with fasterq-dump, I realize I am not 100% sure that I have all the data.
  
  I noticed in my downstream analysis that I seem to be missing the .1 and .2 numbers in the code associated with individual reads with the same spot ID. Then I noticed that my initial fastq file doesn't seem to have those either.
  
  So I'm wondering if the -split-spot option that I used is doing what I want it do do, which is 'get all the sequence data', and how does it differ from --concatenate-reads. I am afraid I did not understand this from the program description. Please help?
  
  **Tags:** fastq, sratoolkit
  
  > **Comments:**
  > **username_1**: Hi username_0, do you have paired-end reads? Can you provide the SRA accession too?  
  > **username_0**: @username_1 It looks like they're paired. Eg. SRR6462984.63.1 and SRR6462984.63.2 .  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-10-24. Score: 3 | Accepted answer
  
  Fasterq comes from the latest version of sratools. So if you check the [manual](https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump) , it says the equivalence is:
  
  > fastq-dump SRRXXXXXX --split-3 --skip-technical
  >
  > fasterq-dump SRRXXXXXX
  
  In older versions of sratoolkit, if you use fastq-dump without specifying --split-3 for paired-end reads, you get the format mentioned, spotID.1 for forward, spotID.2 for reverse:
  
  ```
  fastq-dump SRR6462984.sra
  more SRR6462984.fastq
  
  ```
  
  You get:
  
  ```
  @SRR6462984.1 1 length=301
  NATCTGCCCGTTCCACATAAACACCGTTAAACATCGATAGAGCGAAATAAAGCTGCTGAGTGATGTGATGATAAAGCTTTTCCGTTCTGACACGATCTTCCATCTCGTCTATCATTGCATCGAGAGCGTCAGAGATCGCAAGCAGTGCGGATATTGCCGTCCGTCTTGAAGCTTTGGCAGAGCCAGGCGGAATTTGTTTATCGGATAGTGTTTATGCGCAAATTTAGCATATGATTTCCGACAACTTTTGCTTCATCGGGCCGCAAAGCGTGAAAAACAGTGTCGTCACCGTTGATGTGTG
  +SRR6462984.1 1 length=301
  #/AAAEE/EEEA/EAAEEAEE/EE/EEA/EEEEE/AAE/EE/EAEAE//EEAEE/EEEEE<EEEEE/EE<EE/AEEEE/EAEEEEA/E<EEAEAEEEEEEAEEEE<EEAEEEEEAAAEEE/EEEEE/E//AEEEE6EA66EE<<<EAAA/AAAAAE/E6E/EA/AE/AEEEEEEAAEEEEA6EEEEEEEEE/EEE/AEEAAAEEEAE/E/EEEEEA//E//EEE/EEE/A<//AE/EE//6A///AA/E//E/E/EE//AE//AAEEE////E/A<AAE/EEAE//A//6/A</<6/</E/
  @SRR6462984.2 2 length=302
  NTCAGCAGGCGCCGTAACTTCAGCAAAACTGTAGCTATAACTTTTCCGAACTTTATACCTAACTTCGCTTTCCTAGCACTGTATAAAATGCCTAAAAGAAATCAGCAGGCGCCGTCACTTCAAAAAATCAGTATGGATCAATCAGACGCGGAGCTTATTAAAACAGAGCTTATTAAAAATTATGTCTTTCTTCTTCTTTCAGCAATTCGCAACGTAAAATTCAAAATTTTGGACGCCGTAATTGCGCAGGAACCAATTCAAAGAGGCGGCGGCCAATTAATTCCAACGTCTCGAAGAGTGGC
  +SRR6462984.2 2 length=302
  
  ```
  
  With the latest version, it by defaults splits the paired end sra file into forward and reverse fastq (i.e --split-3):
  
  ```
  fasterq-dump SRR6462984.sra 
  head -2 SRR6462984_*.fastq
  
  ```
  
  And you get
  
  ```
  ==> SRR6462984_1.fastq <==
  @SRR6462984.1 1 length=150
  NATCTGCCCGTTCCACATAAACACCGTTAAACATCGATAGAGCGAAATAAAGCTGCTGAGTGATGTGATGATAAAGCTTTTCCGTTCTGACACGATCTTCCATCTCGTCTATCATTGCATCGAGAGCGTCAGAGATCGCAAGCAGTGCGG
  
  ==> SRR6462984_2.fastq <==
  @SRR6462984.1 1 length=151
  ATATTGCCGTCCGTCTTGAAGCTTTGGCAGAGCCAGGCGGAATTTGTTTATCGGATAGTGTTTATGCGCAAATTTAGCATATGATTTCCGACAACTTTTGCTTCATCGGGCCGCAAAGCGTGAAAAACAGTGTCGTCACCGTTGATGTGTG
  
  ```
  
  So if you need to get back the .1 and .2 format, use fastq-dump from the latest installation.
  
  I would suggest sticking to the newest format, with 2 files, because fastq-dump will be deprecated in the future.
  
  > **Comments:**
  > **username_2**: Can you have a look at this https://bioinformatics.stackexchange.com/questions/21407/multiple-srr-id-downloaded-for-single-gsm-ids-input-issue  
  
  ---
  
  