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nf-core / riboseq

Pipeline for the analysis of ribosome profiling, or Ribo-seq (also named ribosome footprinting) data.
https://nf-co.re/riboseq
MIT License
6 stars 4 forks source link

Incorporate check for 3nt periodicity #24

Open pinin4fjords opened 6 months ago

pinin4fjords commented 6 months ago

Description of feature

Ensure one of the modules installed can perform this check.

JackCurragh commented 6 months ago

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 commented 6 months ago

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 commented 6 months ago

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 commented 6 months ago

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.