# 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.

• 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. Oct 26 '20 at 18:19