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

Incorporate check for 3nt periodicity #24

Open
pinin4fjords opened this issue Feb 19, 2024 · 4 comments
Open

Incorporate check for 3nt periodicity #24

pinin4fjords opened this issue Feb 19, 2024 · 4 comments
Labels
enhancement New feature or request
Milestone

Comments

@pinin4fjords
Copy link
Member

Description of feature

Ensure one of the modules installed can perform this check.

@pinin4fjords pinin4fjords added the enhancement New feature or request label Feb 19, 2024
@pinin4fjords pinin4fjords added this to the v1.10 milestone Feb 19, 2024
@JackCurragh
Copy link
Contributor

Ribo-Seq data that is prepared with MNase rather than RNase will not pass most 3nt periodicity checks. It doesn't necessarily mean it is poor quality data just that its purposes may be different. For quantification it may be perfectly fine.

3nt periodicity is most important for ORF calling. So this check may be best places a the start of that branch. This is actually once of the most awkward aspects of running RiboCode as it checks this periodicity in quite a naive way.

@pinin4fjords
Copy link
Member Author

Thanks @JackCurragh ! This check was requested by Altos, hence its inclusion here, and ORF calling is at the top of our feature list for V1.

@JackCurragh
Copy link
Contributor

Completely understandable. I would just argue that it's placement within the pipeline can make a big difference to the types of Ribo-Seq libraries we can work with.

Also, my own application RiboMetric would likely have been a good fit for this and many other aspects but even I won't advocate for it's inclusion yet. Once I have done a bit more development and get it on bioconda I will see where it will fit best

@pinin4fjords
Copy link
Member Author

Sounds good- just create the issue so we don't forget.

Bioconda from PyPi is easy. I recommend GraySkull to make you a starting point, and happy to help.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
None yet
Development

No branches or pull requests

2 participants