<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>

CC BY-SA 4.0
2023-08-09T03:37:05.800Z
Can you have a look at this https://bioinformatics.stackexchange.com/questions/21407/multiple-srr-id-downloaded-for-single-gsm-ids-input-issue
PesKchan
CC BY-SA 4.0
2019-10-24T14:26:48.720Z
2019-10-24T14:26:48.720Z
2020-06-18T08:30:41.743Z
StupidWolf
<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>

CC BY-SA 4.0
2019-10-24T11:35:30.207Z
Hi Laura, do you have paired-end reads? Can you provide the SRA accession too?
StupidWolf
CC BY-SA 4.0
2019-10-24T13:05:47.350Z
@StupidWolf It looks like they're paired. Eg. SRR6462984.63.1 and SRR6462984.63.2 .
Laura
<fastq><sratoolkit>
Fasterq-dump: --split-spot or -concatenate-reads?
# 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 Laura, do you have paired-end reads? Can you provide the SRA accession too?  
> **username_0**: @StupidWolf 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 , 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
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  

---

