Hi, I am trying to implement cutadapt. This is the first time i am using the software.
i used fastQC and identified some primers. I have set up the parameters and run the cutadapt to remove these primers before mapping. With the output from cutadapt, I re-run fastQC and this time I get another set of primers.
I used -e 0.01. Does being strict with the error rate affect this?
Am I doing something wrong? Or does this mean I need to rerun the cutadapt until fastQC does not find ant primer/adapter?