<p>The definitive answer is the sequencing institute/lab. They know what protocol/chemistry etc. was used.</p>
<p>If you don't have access to that a number of tools check for known adapter sequences. Run e.g. <a href="https://www.bioinformatics.babraham.ac.uk/projects/fastqc/" rel="nofollow noreferrer">FASTQC</a>, which will tell you the proportions of adapter sequence found. Tools like <a href="https://github.com/FelixKrueger/TrimGalore" rel="nofollow noreferrer">TrimGalore</a> can also autodetect the most common adapters.</p>
<p>UPDATE:
I checked 2M reads from one run of your dataset and it seems to me that it was uploaded already preprocessed:</p>
<p><a href="https://i.sstatic.net/MY5qw.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/MY5qw.png" alt="per-sequence-quality" /></a>
<a href="https://i.sstatic.net/C6keF.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/C6keF.png" alt="length-distribution" /></a>
<a href="https://i.sstatic.net/eLvPC.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/eLvPC.png" alt="adapter-content" /></a></p>
<p>Check all your samples, but I don't see a need to do any preprocessing if all of them look like this.</p>

CC BY-SA 4.0
2020-10-26T17:53:32.437Z
Thank you! @BastianSchiffthaler. That was helpful. I wanted to make matrix table of these read, how can I join columns of these read into one table in this case? because I tried to make them collection, it failed. also when you uploaded them did you upload them as fastqsanger.gz or as different format?
user432797
CC BY-SA 4.0
2020-10-26T17:55:45.717Z
I updated the question with the photo of table that want to make (it is an example not the real data that I linked) @BastianSchiffthaler
user432797
CC BY-SA 4.0
2020-10-26T18:19:14.240Z
I would say this is really a separate question, but essentially the easiest pipeline is: Download the fastq.gz, run [salmon](https://github.com/COMBINE-lab/salmon) with a human reference (there are tons of tutorials for this). In `R`, use the [tximport](https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html) package to create a count matrix.
Bastian Schiffthaler
CC BY-SA 4.0
2020-10-26T18:21:34.227Z
Thank you @BastianSchiffthaler. I used join column on collection in galaxy, why it did not work? I want to do it in galaxy.
user432797
CC BY-SA 4.0
2020-10-26T18:33:50.210Z
Sorry, can't help you there, I don't use Galaxy. Please submit a new question for this so you get help.
Bastian Schiffthaler
CC BY-SA 4.0
2020-10-26T10:25:55.093Z
2020-10-26T11:12:17.440Z
2020-10-26T11:12:17.440Z
Bastian Schiffthaler
<p>I have this GSE dataset ( GSE104279 ) (<a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE104279" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE104279</a>)</p>
<p>I want to run cutadapt, but how would I find the adapter sequence so I can run cutadapt?</p>
<p><a href="https://i.sstatic.net/6RMNp.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/6RMNp.png" alt="enter image description here" /></a></p>

<rna-seq><phylogenetics>
How to find adapter sequence
# How to find adapter sequence

(Asked by: username_0 on 2020-10-25)

I have this GSE dataset ( GSE104279 ) (<https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE104279>)

I want to run cutadapt, but how would I find the adapter sequence so I can run cutadapt?

[![enter image description here](https://i.sstatic.net/6RMNp.png)](https://i.sstatic.net/6RMNp.png)

**Tags:** rna-seq, phylogenetics

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## 1 answers

### Answer by username_1 on 2020-10-26. Score: 4 | Accepted answer

The definitive answer is the sequencing institute/lab. They know what protocol/chemistry etc. was used.

If you don't have access to that a number of tools check for known adapter sequences. Run e.g. [FASTQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), which will tell you the proportions of adapter sequence found. Tools like [TrimGalore](https://github.com/FelixKrueger/TrimGalore) can also autodetect the most common adapters.

UPDATE:
I checked 2M reads from one run of your dataset and it seems to me that it was uploaded already preprocessed:

[![per-sequence-quality](https://i.sstatic.net/MY5qw.png)](https://i.sstatic.net/MY5qw.png)
[![length-distribution](https://i.sstatic.net/C6keF.png)](https://i.sstatic.net/C6keF.png)
[![adapter-content](https://i.sstatic.net/eLvPC.png)](https://i.sstatic.net/eLvPC.png)

Check all your samples, but I don't see a need to do any preprocessing if all of them look like this.

> **Comments:**
> **username_0**: Thank you! @BastianSchiffthaler. That was helpful. I wanted to make matrix table of these read, how can I join columns of these read into one table in this case? because I tried to make them collection, it failed. also when you uploaded them did you upload them as fastqsanger.gz or as different format?  
> **username_0**: I updated the question with the photo of table that want to make (it is an example not the real data that I linked) @BastianSchiffthaler  
> **username_1**: I would say this is really a separate question, but essentially the easiest pipeline is: Download the fastq.gz, run [salmon](https://github.com/COMBINE-lab/salmon) with a human reference (there are tons of tutorials for this). In `R`, use the [tximport](https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html) package to create a count matrix.  
> **username_0**: Thank you @BastianSchiffthaler. I used join column on collection in galaxy, why it did not work? I want to do it in galaxy.  
> **username_1**: Sorry, can't help you there, I don't use Galaxy. Please submit a new question for this so you get help.  

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