No adapter removal despite Adapter Content Fail in FastQC report
Created by: nnordhol
Hi,
Nice to see you were able to integrate the MT only-mode in 1.3. The preprocessing would fail to recognise that adapters were present (as reported by FastQC) and skip adapter removal. I think I identified the problem in preprocess.py: the has_adapter() function checks for over represented sequences when it should check for "Adapter Content" in the FastQC report. Changing the function as below solved it for me and would be the correct way to identify whether adapters are present from FastQC report:
def has_adapters(self, fastqc_report): data = parse_fastqc(fastqc_report) if data['Adapter Content'][0] == 'pass': return False else: return True
Best, Niclas