I am using Cutadapt, but I have a problem: It doesn't find adapter, but with a banal research with function "find" in the file I find adapters, so I am sure that they are in my file.
Probabily the problem is in the parameters that I wrote. In particular I have a list of adapterand I have to trim at 5'. I wrote this:
cutadapt -g adapter.fasta -o output.fastq myfile.fastq
What is the problem? Please could you help me?
Thank you in advance.