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

Updating the default V4 EMP primers #17

Open
mestaki opened this issue Oct 19, 2021 · 1 comment
Open

Updating the default V4 EMP primers #17

mestaki opened this issue Oct 19, 2021 · 1 comment

Comments

@mestaki
Copy link
Contributor

mestaki commented Oct 19, 2021

Just noticed that the V4 primers being used in the weight assembly scripts are using the old EMP primers (ex here). A few years back these were modified slightly and degeneracy added (as described here). I'm not sure if this would have any real significant effect but might be worth updating nevertheless.

Primers currently being used in weight assembly:
FWD: GTGCCAGCMGCCGCGGTAA
REV: GGACTACHVGGGTWTCTAAT

Recommended update to new EMP primers:
FWD: GTGYCAGCMGCCGCGGTAA;
REV: GGACTACNVGGGTWTCTAAT

@nbokulich
Copy link
Collaborator

I agree, definitely worth updating!

The effect on weights would probably be minor, but the newer primers are presumably what most new studies would be using, so important to update.

mestaki added a commit to mestaki/readytowear that referenced this issue Oct 21, 2021
Addresses BenKaehler#17 which clarifies that the V4 specific reads are likely in the right orientation, though not tested.
mestaki added a commit to mestaki/readytowear that referenced this issue Oct 21, 2021
Addresses BenKaehler#17 which clarifies that the V4 specific reads are likely in the right orientation, though not tested.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants