How to find adapter sequence 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?
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:



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