Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-10-26T17:53:32.437Z
Answers.Text: 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?
Answers.UserDisplayName: user432797
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-10-26T17:55:45.717Z
Answers.Text: 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
Answers.UserDisplayName: user432797
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Answers.CreationDate: 2020-10-26T18:19:14.240Z
Answers.Text: 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.
Answers.UserDisplayName: Bastian Schiffthaler
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-10-26T18:21:34.227Z
Answers.Text: Thank you @BastianSchiffthaler. I used join column on collection in galaxy, why it did not work? I want to do it in galaxy.
Answers.UserDisplayName: user432797
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-10-26T18:33:50.210Z
Answers.Text: Sorry, can't help you there, I don't use Galaxy. Please submit a new question for this so you get help.
Answers.UserDisplayName: Bastian Schiffthaler
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Answers.LastEditDate: 2020-10-26T11:12:17.440Z
Answers.UserDisplayName: Bastian Schiffthaler
Body: <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>
  
Tags: <rna-seq><phylogenetics>
Title: How to find adapter sequence
ThreadText: # 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
  
  
  ---
  
  ## 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! @username_1. 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) @username_1  
  > **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 @username_1. 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.  
  
  ---
  
  