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


1 Answer 1


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, which will tell you the proportions of adapter sequence found. Tools like 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 length-distribution adapter-content

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

  • $\begingroup$ 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? $\endgroup$
    – user432797
    Oct 26, 2020 at 17:53
  • $\begingroup$ 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 $\endgroup$
    – user432797
    Oct 26, 2020 at 17:55
  • 2
    $\begingroup$ I would say this is really a separate question, but essentially the easiest pipeline is: Download the fastq.gz, run salmon with a human reference (there are tons of tutorials for this). In R, use the tximport package to create a count matrix. $\endgroup$ Oct 26, 2020 at 18:19
  • $\begingroup$ Thank you @BastianSchiffthaler. I used join column on collection in galaxy, why it did not work? I want to do it in galaxy. $\endgroup$
    – user432797
    Oct 26, 2020 at 18:21
  • 2
    $\begingroup$ Sorry, can't help you there, I don't use Galaxy. Please submit a new question for this so you get help. $\endgroup$ Oct 26, 2020 at 18:33

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