Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

N wildcards should not be counted when computing the error rate #360

Closed
marcelm opened this issue Feb 26, 2019 · 0 comments

Comments

@marcelm
Copy link
Owner

commented Feb 26, 2019

In a match of an adapter containing N wildcards against the read, the wildcards should not contribute to the length. For example, if adapter CCNCCC is matched to CCTCAC then the error rate should be computed as 1/5=0.2 because there is one mismatch in five non-N bases.

Otherwise, adapter sequences such as ACGTN{20} have an unexpectedly high number of allowed errors.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
1 participant
You can’t perform that action at this time.