I would like to use cutadapt and/or trimmomatic to trim my sequences. I'm usually analyzing data from GEO or Array Express, and it's not always possible to get information about adaptors. Also, it's not always possible to trust information provided there...
I can see that fastQC detects adaptor sequences, including those with a slightly different sequence. So I'm thinking there should be a way to trim adaptors automatically, without knowing their sequence or name?
Thanks for tips
Edit: just found out FastQC uses a file called "contaminant_list.txt". I guess I could write some script to look for these adapters in my data, but I'm not sure it's the best way to go though.